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GROMACS 5.0.x CUDA/GPU Detection Failure With Ubuntu 14.04 nVidia 331.113 Update – Fix With An apt-get

Saturday, January 3rd, 2015

If not for the near-20x speedup I’ve achieved running GROMACS on an nVidia GTX 770 Classified over an Intel i7 Extreme 6-core, nVidia in Ubuntu would almost be more trouble than its worth. The initial installation of the nVidia drivers from the nVidia website works, then the first time Ubuntu auto-updates the drivers to the latest-and-greatest, you’re never entirely sure what the next boot is going to look like – usually a black screen at best. And, if you found this page while looking for a solution to the nVidia driver update black/blank screen, my solution (which has worked without issue to date) is to ditch lightdm and use the GNOME Display Manager (gdm) instead (this apparently appears to be a theme with Ubuntu 14.04 installs on SSD drives as well).

sudo apt-get install gdm

Now, with that settled, the latest update (331.113) broke my GROMACS GPU install (performed using the steps outlined at: GROMACS 5.0.1, nVidia CUDA Toolkit, And FFTW3 Under Ubuntu 14.04 LTS (64-bit); The Virtues Of VirtualBox). The error for my system looks as follows:

GROMACS:      gmx mdrun, VERSION 5.0.1
Executable:   /opt/gromacs_gpu/bin/gmx
Library dir:  /opt/gromacs_gpu/share/gromacs/top
Command line:
  gmx mdrun -v -deffnm RUN_solv_em -s RUN_ions.tpr -o RUN_em.trr -gpu_id 0


NOTE: Error occurred during GPU detection:
      unknown error
      Can not use GPU acceleration, will fall back to CPU kernels.

Reading file RUN_ions.tpr, VERSION 5.0.1 (single precision)
Using 1 MPI thread
Using 12 OpenMP threads 

That said, nvidia-smi sees all three cards in my system just fine.

+------------------------------------------------------+                       
| NVIDIA-SMI 331.113    Driver Version: 331.113        |                       
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|===============================+======================+======================|
|   0  GeForce GTX 650     Off  | 0000:01:00.0     N/A |                  N/A |
| 21%   30C  N/A     N/A /  N/A |    183MiB /  1023MiB |     N/A      Default |
+-------------------------------+----------------------+----------------------+
|   1  GeForce GTX 770     Off  | 0000:02:00.0     N/A |                  N/A |
| 35%   29C  N/A     N/A /  N/A |      9MiB /  4095MiB |     N/A      Default |
+-------------------------------+----------------------+----------------------+
|   2  GeForce GTX 770     Off  | 0000:03:00.0     N/A |                  N/A |
| 35%   25C  N/A     N/A /  N/A |      9MiB /  4095MiB |     N/A      Default |
+-------------------------------+----------------------+----------------------+
                                                                               
+-----------------------------------------------------------------------------+
| Compute processes:                                               GPU Memory |
|  GPU       PID  Process name                                     Usage      |
|=============================================================================|
|    0            Not Supported                                               |
|    1            Not Supported                                               |
|    2            Not Supported                                               |
+-----------------------------------------------------------------------------+

Concerned that this might be some kind of issue with the drivers and my compiled version of 5.0.1, I compiled a copy of 5.0.4 using the same build parameters in cmake. The result? Same problem.

The simple solution (which may apply to all things OpenCL as well, but my concern was simply GROMACS) is to install nvidia-modprobe.

sudo apt-get install nvidia-modprobe

Whatever happened in the install, GROMACS now sees the GPU cards just fine.

GROMACS:      gmx mdrun, VERSION 5.0.4
Executable:   /opt/gromacs_gpu_504/bin/gmx
Library dir:  /opt/gromacs_gpu_504/share/gromacs/top
Command line:
  gmx mdrun -v -deffnm RUN_solv_em -s RUN_ions.tpr -o RUN_em.trr -gpu_id 0

Reading file RUN_md.tpr, VERSION 5.0.4 (single precision)

Using 1 MPI thread
Using 12 OpenMP threads 

3 GPUs detected:
  #0: NVIDIA GeForce GTX 770, compute cap.: 3.0, ECC:  no, stat: compatible
  #1: NVIDIA GeForce GTX 650, compute cap.: 3.0, ECC:  no, stat: compatible
  #2: NVIDIA GeForce GTX 770, compute cap.: 3.0, ECC:  no, stat: compatible

0 GPU user-selected for this run.
Mapping of GPU to the 1 PP rank in this node: #0

“OrtVc1 failed #1.” Workaround In Gaussian09; Warning About (Pre-)Resonance Raman Spectra In GaussView 4/5

Thursday, January 1st, 2015

And Happy New Year.

Two issues (one easily addressable, one only by external workaround) related to the prediction of Raman intensities in Gaussian09 – for which there’s next-to-nothing online to address either of them (likely because they don’t come up that often).

OrtVc1 failed #1.

In simulating the Raman spectra of very long (> C60) polyenes as a continuance of work related to the infinite polyacetylene case (see this post for details: Bond Alternation In Infinite Periodic Polyacetylene: Dynamical Treatment Of The Anharmonic Potential), I reached a length and basis set for which Gaussian provides the following output and error:

...
 Minotr:  UHF open shell wavefunction.
          Direct CPHF calculation.
          Differentiating once with respect to electric field.
                with respect to dipole field.
          Electric field/nuclear overlap derivatives assumed to be zero.
          Using symmetry in CPHF.
          Requested convergence is 1.0D-08 RMS, and 1.0D-07 maximum.
          Secondary convergence is 1.0D-12 RMS, and 1.0D-12 maximum.
          NewPWx=F KeepS1=T KeepF1=T KeepIn=T MapXYZ=F SortEE=F KeepMc=T.
          MDV=    3932153962 using IRadAn=       1.
 Generate precomputed XC quadrature information.
          Solving linear equations simultaneously, MaxMat=      72.
          There are     3 degrees of freedom in the 1st order CPHF.  IDoFFX=0 NUNeed=     3.
      3 vectors produced by pass  0 Test12= 3.94D-11 3.33D-08 XBig12= 2.15D+05 2.71D+02.
 AX will form     3 AO Fock derivatives at one time.
 FoFJK:  IHMeth= 1 ICntrl=       0 DoSepK=F KAlg= 0 I1Cent=   0 FoldK=F
 IRaf= 160000000 NMat=   3 IRICut=       1 DoRegI=T DoRafI=F ISym2E=-1.
 FoFCou: FMM=T IPFlag=           0 FMFlag=      100000 FMFlg1=        2001
         NFxFlg=           0 DoJE=F BraDBF=F KetDBF=F FulRan=T
         wScrn=  0.000000 ICntrl=       0 IOpCl=  1 I1Cent=           0 NGrid=           0
         NMat0=    3 NMatS0=      3 NMatT0=    0 NMatD0=    3 NMtDS0=    0 NMtDT0=    0
 Petite list used in FoFCou.
 FMM levels:  10  Number of levels for PrismC:   9
      3 vectors produced by pass  1 Test12= 3.94D-11 3.33D-08 XBig12= 1.52D+04 3.94D+01.
      3 vectors produced by pass  2 Test12= 3.94D-11 3.33D-08 XBig12= 1.29D+04 3.31D+01.
      3 vectors produced by pass  3 Test12= 3.94D-11 3.33D-08 XBig12= 1.65D+06 4.27D+01.
      3 vectors produced by pass  4 Test12= 3.94D-11 3.33D-08 XBig12= 1.92D+08 6.96D+02.
      3 vectors produced by pass  5 Test12= 3.94D-11 3.33D-08 XBig12= 4.40D+10 7.74D+03.
      3 vectors produced by pass  6 Test12= 3.94D-11 3.33D-08 XBig12= 4.42D+12 1.70D+05.
      3 vectors produced by pass  7 Test12= 3.94D-11 3.33D-08 XBig12= 3.50D+14 1.14D+06.
      3 vectors produced by pass  8 Test12= 3.94D-11 3.33D-08 XBig12= 3.13D+16 1.34D+07.
      3 vectors produced by pass  9 Test12= 3.94D-11 3.33D-08 XBig12= 1.75D+18 4.02D+07.
      3 vectors produced by pass 10 Test12= 3.94D-11 3.33D-08 XBig12= 1.28D+20 7.81D+08.
      3 vectors produced by pass 11 Test12= 3.94D-11 3.33D-08 XBig12= 1.50D+22 7.70D+09.
      3 vectors produced by pass 12 Test12= 3.94D-11 3.33D-08 XBig12= 1.12D+24 5.57D+10.
      3 vectors produced by pass 13 Test12= 3.94D-11 3.33D-08 XBig12= 2.86D+25 5.87D+11.
 OrtVc1:  Ph=1 IOff=     0 IPass=20 DotMx1= 2.08D-06
 OrtVc1:  Ph=1 M=  1181528 NPass=20 Test1= 3.94D-11 Small= 1.18D-06 VSmall= 1.00D-12
 OrtVc1 failed #1.
 Error termination via Lnk1e in /opt/g09/l1002.exe at Sat Oct 11 01:10:22 2014.

What little there is available online for the “OrtVc1 failed #1.” error (from CCL – here and here) is less than helpful in addressing the problem. The problem is also coordinate system-independent (Cartesian and z-matrix formats both provide the same error), but is sensitive to the choice of basis set (6-31G(d,p) would work fine through the Raman intensity predictions, 6-311G(2d,p) would fail at the stage above).

Directing the issue to Gaussian, the provided workaround is straightforward.

The prediction of Raman intensities requires using Coupled Perturbed Hartree-Fock (CPHF), for which a special sensitivity in the code (currently) exits when using both molecular symmetry and the fast multipole method, the use of which (FMM, that is) is governed by Gaussian09 based on the atom count.

The workaround, provided by Dr. Fernando Clemente at Gaussian, Inc., is to divide the calculation into two steps. My input for the first successful run is shown below. A few details:

1. The first stage contains no Raman keywords (just the plain “freq” call).

2. In the second stage, the cphf=rdfreq is reading an incident light frequency of 0 (cm-1 or nm) at the bottom of the input file (“0”). You can run the static or dynamic cases as you like at this stage.

3. Also in the second stage, FMM is turned off (nofmm).

4. Also still in the second stage, the option to calculate Raman intensities is turned on (polar=raman). This is, as it happens, a recommended way to perform Raman intensity calculations – run a typical normal mode analysis, then import the force constants (and geometry) from this calculation into a Link1 step while increasing the basis set size (for better intensity prediction).

%chk=checkpoint.chk
%nprocshared=12
%mem=50000MB
#p integral(grid=ultrafine) freq=hpmodes b3lyp/6-311++g(3df,3pd) scf=novaracc symm=loose

Part 1 - just the frequency calculation

0 1
 C                  0.00000000   48.56668920   -0.34496298
 C                  0.00000000   47.35252242    0.35603740
...
 H                  0.00000000  -49.50718415    0.19804614
 H                 -0.00000000   49.50718415    0.19804614
[blank line 1]
[blank line 2]
--link1--
%chk=checkpoint.chk
%nprocshared=12
%mem=50000MB
#p integral(grid=ultrafine) polar=raman cphf=rdfreq nofmm b3lyp/6-311++g(3df,3pd) geom=checkpoint

Part 2 - Raman intensities

0 1

0
[blank line 1]
[blank line 2]

In theory, your calculation should run just fine.

Raman Intensities And GaussView – Check Your .log File For Resonance

The next problem is GaussView-specific – one that only comes up when you’ve a system with dynamic polarizability (incredibly long polyenes being a prototypical example) or when you perform frequency-dependent Raman calculations and you slip near resonance.

When running a series of Raman intensity calculations with increasing incident light frequency (cphf=rdfreq, then an array of energies), Mode 17 of this particular molecule either has a really large activity (cannot be printed out) or we’re approaching resonance (also a case of really large activity and it can’t be printed out). This isn’t a problem with the code, it’s your molecule.

                     16                     17                     18
                     BG                     AG                     BG
 Frequencies --    218.8851               257.7857               266.9993
 Red. masses --      3.5318                 5.1372                 2.2022
 Frc consts  --      0.0997                 0.2011                 0.0925
 IR Inten    --      0.0000                 0.0000                 0.0000
 Raman Activ --      0.2046                 0.7412                 0.2871
 Depolar (P) --      0.7500                 0.3044                 0.7500
 Depolar (U) --      0.8571                 0.4667                 0.8571
 RamAct Fr= 1--      0.2046                 0.7412                 0.2871
  Dep-P Fr= 1--      0.7500                 0.3044                 0.7500
  Dep-U Fr= 1--      0.8571                 0.4667                 0.8571
...
 RamAct Fr=12--     90.1095           ************                 0.3406
  Dep-P Fr=12--      0.7500                 0.3333                 0.7500
  Dep-U Fr=12--      0.8571                 0.4999                 0.8571

This is all well-and-good if you only rely on the .log file. If you skip the .log file inspection and only ever use GaussView, the result of inspecting the Raman intensities is below.

2015jan1_Mode17_Wrong_Raman_Activity

Note that Mode 17 has the intensity of Mode 18, and Mode 18 has zero intensity. Something is afoot! If you know what to expect out of your system, the missing intensities should be obvious. If not, you’re missing some very important information about your molecule.

The GaussView developers are aware of the problem. In the meantime, you can get around this problem by globally replacing all of the ” ************ ” (note the spaces on either side!) with a huge number (at which point the Raman intensity issue will become obvious – careful to preserve the spacing in the .log file).

The EMSL Basis Set Exchange 6-31G, 6-31G(d), And 6-31G(d,p) Gaussian-Type Basis Set For CRYSTAL88/92/95/98/03/06/09/14/etc. – Conversion, Validation With Gaussian09, And Discussion

Tuesday, December 30th, 2014

Jump to the basis sets and downloadable files here: files, 6-31G, 6-31Gd, 6-31Gdp.

If you use these results: Please drop me a line (damian@somewhereville.com), just to keep track of where this does some good. That said, you should most certainly cite the EMSL and Basis Set references at the bottom of this page.

It’s a fair bet that Sir John Pople would be the world’s most cited researcher by leaps and bounds if people properly cited their use of the basis sets he helped develop.

The full 6-31G, 6-31G(d), and 6-31G(d,p) series (yes, adding 6-31G(d) is a bit of a cheat in this list) from the EMSL Basis Set Exchange is presented here in the interest of giving the general CRYSTALXX (that’s CRYSTAL88, CRYSTAL92, CRYSTAL95, CRYSTAL98, CRYSTAL03, CRYSTAL06, CRYSTAL09, now CRYSTAL14 – providing the names here for those who might be searching by version) user a “standard set” of basis sets that are, for the most part, the same sets one does / could employ in other quantum chemistry codes (with my specific interest being the use and comparison of Gaussian and GAMESS-US in their “molecular” (non-solid-state) implementations). Members of the CRYSTAL developer team provide a number of basis sets for use with the software. While this is good, I will admit that I cannot explain why the developers chose not to include three of the four most famous basis sets in all of (all of) computational chemistry – 3-21G (upcoming), 6-31G(d,p) (presented here), and 6-311G(d,p) (also upcoming).

More “But why?” There are, generally, many basis sets available for most of the Periodic Table in the CRYSTALXX Basis Set Library. In terms of consistency across all calculations to the molecular-centric quantum chemist, the 6-31G(d,p) series is the cut-off family of basis sets for many, many projects in all computational chemistry research – the series is just large enough to provide predictions “good enough” for publication but is also small enough that systems will properly optimize in a reasonable amount of time for standalone use or as “beautification” calculations for larger basis set studies (this is specifically true for crystal structure optimizations, as considerable time can be wasted simply “cleaning up” hydrogen atom (R-H) bond lengths, which are notoriously underestimated by approx. 10% in X-ray studies (but neutron methods give poorer lattice constants generally, so you can’t win for quick clean-ups either way)). Furthermore, 6-31G(d,p) is the “B3LYP” of basis sets – one that most everyone has used in structure optimizations and one that is constantly run across in computational quantum chemistry studies among typical non-hard-theory quantum chemists (which is not meant to be a slight to the broader user base using computational chemistry for its interpretive value – it’s my workhorse basis set for many past studies). These two points drove the conversion all of the published 6-31G(d,p) basis set data to CRYSTALXX to have it generally available as a solid-state density functional theory (DFT) tool.

This blog post doesn’t reinvent any wheels and, therefore, isn’t something I consider worth submitting for journal publication. That said, having these basis sets is better than not, so the complete set and analysis is provided below. But first…

Note 1: Trust But Verify; RHF

When one thinks of the variational principle, one doesn’t often see the choice of software as being a mechanism to a achieve a lowest energy for a system. While it would be really nice if each program agreed on the lowest energy for a basis set (which, theoretically, seems like it would be the correct result), different programs use different approximations, internal tools, and convergence methodologies to “reach bottom.” Within the same code, these approximations, tools, and methods are, assumedly, “internally consistent” and, obviously, it is safe to compare those apples and apples on Apples.

For those looking for a more detailed study of the differences (by energy) of various quantum chemistry codes, I direct your attention to – Journal of Molecular Structure: THEOCHEM 768 (2006) 175–181 (Concerning the precision of standard density functional programs: GAUSSIAN, MOLPRO, NWCHEM, Q-CHEM, and GAMESS), a paper I stared at for many minutes in trying to come to grips with the energy comparisons when I first started the testing.

Obviously, just presenting coefficients on a blog post and expecting people to trust their use blindly for peer-review publications is a non-starter. Simply doing the conversion itself for in-house studies without some kind of comparison to other energies with tested formats is also a non-starter, as a single wrong number or exponent throws the whole basis set into question (and, admittedly, I fought for several days with helium energies before discovering I’d … misplaced one electron in the conversion process). Therefore, part of the conversion process includes a series of tests comparing the results of Gaussian09 and CRYSTAL09 (not timing tests, simply final energies in an attempt to get the CRYSTAL09 energies to look like the other energies enough to trust that the basis set conversion was successful).

What you learn from performing this type of study is the extent to which quantum chemistry codes can differ significantly in their treatment of integrals, functionals, grids, and convergence criteria. As a way out of part of these problems, the best way to perform comparisons is to run good olde Restricted Hartree-Fock (RHF) calculations, avoiding functional and grid size specifications. Convergence methods and integral treatment may still differ, but it’s possible to get agreement between Gaussian09 and CRYSTAL09 to within 10^-9 Hartree (and even this can get better).

Routinely hitting very small energy differences is my way of believing the correctness of the basis set conversions, but I provide all of the files associated with this project below for your own analyses. You are, of course, welcome to (and encouraged to) perform some sample runs of your own before setting out on a full computational project.

NOTE 2: B3LYP vs. B3LYP

As only becomes obvious after many unsuccessful trials and keyword tweaking, Gaussian’s default B3LYP is NOT the default B3LYP used in GAMESS-US and CRYSTALXX (this going back to a long involved discussion of VWN forms). In short – Gaussian’s B3LYP employes the VWN3 electron gas correlation functional, while GAMESS and CRYSTAL09 use the VWN5 electron gas correlation functional in their default implementations. To get Gaussian to run B3LYP with VWN5, the following keyword set is required (this is old hat in the community and is reported on several websites):

bv5lyp iop(3/76=1000002000) iop(3/77=0720008000) iop(3/78=0810010000)

You can interpret this as:

Functional Form Call:
(Becke exchange/VWN5 local correlation/LYP non-local correlation)
HF Exchange: (20% HF exchange) +
DF Exchange: (72% Becke non-local exchange + 80% Slater local exchange) +
Correlation: (81% LYP non-local correlation + 100% V5LYP VWN5 local correlation).

How much does this matter to the energy calculations? Plenty. Here are comparison energies for the Noble Gases using the two functionals and the 6-31G(d,p) out of Gaussian (using the internal 6-31G(d,p) basis set, program option “ultrafine” grid size and program option “tight” convergence criteria):

Element
B3LYP Energy
(Hartree)
B5LYP Energy
(Hartree)
Helium
-2.90704897
-2.89992035
Neon
-128.89435995
-128.85600282
Argon
-527.51714191
-527.44754502

And these differences are for single atoms. The He might look OK-ish to untrained eyes, but the Ar numbers differ by 182.7 kJ/mol (that’s approaching half a C-C bond worth of energy – nothing to attempt comparisons with), showing that these are two very different density functionals.

NOTE 3: A Slight Aside For The Gaussian User

If you’re performing multiple operations in a single input file (and I don’t mean the use of “—Link1—” – I mean optimization and frequency calculations in the same Link0. If you see Gaussian rehash the top of the log file in a run after an operation as if it were running a new file, that’s a new operation), you learn the hard way that “iop” keywords do NOT carry over property prediction operations in Gaussian calculations.

The two sets of frequencies for H2 below are NOT the same. The first employs an opt+freq combination in the same Link0. The input file with the alternatively-defined B3LYP density functional…

%Chk=H2.chk
#p bv5lyp iop(3/76=1000002000) iop(3/77=0720008000) iop(3/78=0810010000) 6-31g(d,p) integral(grid=ultrafine) scf=tight opt=tight freq

H2 optimization and normal mode analysis

0 1
H 0.000 0.000 0.000
H 1.000 0.000 0.000

Produces:

 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
 activities (A**4/AMU), depolarization ratios for plane and unpolarized
 incident light, reduced masses (AMU), force constants (mDyne/A),
 and normal coordinates:
                      1
                     SGG
 Frequencies --   4451.2678
 Red. masses --      1.0078
 Frc consts  --     11.7653
 IR Inten    --      0.0000
  Atom  AN      X      Y      Z
     1   1     0.00   0.00   0.71
     2   1     0.00   0.00  -0.71

The same input file with a Link1 to properly recall the alternatively-defined B3LYP density functional…

%chk=H2.chk
#p bv5lyp iop(3/76=1000002000) iop(3/77=0720008000) iop(3/78=0810010000) 6-31g(d,p) integral(grid=ultrafine) scf=tight opt=tight

H2 optimization

0 1
H 0.000 0.000 0.000
H 1.000 0.000 0.000

–Link1–
%chk=H2.chk
# bv5lyp iop(3/76=1000002000) iop(3/77=0720008000) iop(3/78=0810010000) 6-31G(d,p) freq guess=read geom=check

H2 normal mode analysis

0 1

Produces:

 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
 activities (A**4/AMU), depolarization ratios for plane and unpolarized
 incident light, reduced masses (AMU), force constants (mDyne/A),
 and normal coordinates:
                      1
                     SGG
 Frequencies --   4461.8907
 Red. masses --      1.0078
 Frc consts  --     11.8215
 IR Inten    --      0.0000
  Atom  AN      X      Y      Z
     1   1     0.00   0.00   0.71
     2   1     0.00   0.00  -0.71

Which means what? If you run and opt + freq in the same input file keyword series, the opt will read the iop settings but the freq will ignore them (which I find to be mildly ridiculous). For those keeping track, the 4451 cm-1 mode is the energy of the vibration at the B3LYP/6-31G(d,p) level for an H2 molecule whose H-H bond length is that of the alternatively-defined B3LYP density functional. Run an opt + freq with iop specs for the functional, you need to either use a compound input file format (below) or be ready to run, for instance, a freq calculation by taking the coordinates from the optimization calculation, doing so in two separate Gaussian calculations. Your compound input file would look like the one above.

NOTE 4: What The CRYSTAL Website Has To Say About Reproducing Gaussian Numbers

The CRYSTAL FAQ (as of 2014 Jan 14) states the following concerning the reproduction of Gaussian/CRYSTAL results with CRYSTAL/Gaussian.

> Gaussian 98 - CRYSTAL03 energy 


> If I run Gaussian 98 using the input generated by CRYSTAL03 with the keyword
> GAUSS98 I do not obtain the same energy. What is the problem?


> There are 3 main differences between a standard CRYSTAL run and a GAUSSIAN run.

1. CRYSTAL adopts by default bypolar expansion to compute coulomb integrals when the two distributions do not overlap. 
Insert keyword NOBIPOLA to compute all 2 electron integrals exactly; 

2. CRYSTAL adopts a basis set with 5D and 7F AO; 

3. CRYSTAL adopts the NIST conversion factor bohr/Angstrom CODATA98. Insert the keyword BOHRANGS, followed by the conversion factor adopted by Gaussian

As test cases to show what keywords needs to be included for each calculation, they provide the following neopentane example (using the same geometry for both, with the CRYSTAL geometry symmetrized to unique atoms) at the RHF level (avoiding the DFT issues altogether).

The CRYSTAL input is as follows:

Neopentane
MOLECULE
44
3
6       0.000000000     0.000000000     0.000000000
6       0.893151756     -0.893151756    0.893151756
1       1.551948982     -0.296135169    1.551948982
BOHRANGS
0.529177249
END
6 4
0 0 6 2.0 1.0
   .3047524880D+04   .1834737130D-02
   .4573695180D+03   .1403732280D-01
   .1039486850D+03   .6884262220D-01
   .2921015530D+02   .2321844430D+00
   .9286662960D+01   .4679413480D+00
   .3163926960D+01   .3623119850D+00
0 1 3 4.0 1.0
   .7868272350D+01  -.1193324200D+00   .6899906660D-01
   .1881288540D+01  -.1608541520D+00   .3164239610D+00
   .5442492580D+00   .1143456440D+01   .7443082910D+00
0 1 1 0.0 1.0
   .1687144782D+00   .1000000000D+01   .1000000000D+01
0 3 1 0.0 1.0
   .8000000000D+00   .1000000000D+01
1 3
0 0 3 1.0 1.0
   .1873113696D+02   .3349460434D-01
   .2825394365D+01   .2347269535D+00
   .6401216923D+00   .8137573262D+00
0 0 1 0.0 1.0
   .1612777588D+00   .1000000000D+01
0 2 1 0.0 1.0
   .1100000000D+01   .1000000000D+01
99 0
GAUSS98
END
TOLINTEG
20 20 20 20 20
NOBIPOLA
END
FMIXING
30
TOLDEP
8 
END

And the following is for Gaussian (but, I believe, provided by a CRYSTAL run):

# RHF/GEN 5D 7F GEOM=COORD TEST GFPRINT

Neopentane                                                                      

 0 1
   6  0.0000000000000E+00  0.0000000000000E+00  0.0000000000000E+00
   6  8.9315175600000E-01 -8.9315175600000E-01  8.9315175600000E-01
   6 -8.9315175600000E-01  8.9315175600000E-01  8.9315175600000E-01
   6  8.9315175600000E-01  8.9315175600000E-01 -8.9315175600000E-01
   6 -8.9315175600000E-01 -8.9315175600000E-01 -8.9315175600000E-01
   1  1.5519489820000E+00 -2.9613516900000E-01  1.5519489820000E+00
   1 -1.5519489820000E+00  2.9613516900000E-01  1.5519489820000E+00
   1  1.5519489820000E+00  2.9613516900000E-01 -1.5519489820000E+00
   1 -1.5519489820000E+00 -2.9613516900000E-01 -1.5519489820000E+00
   1  1.5519489820000E+00  1.5519489820000E+00 -2.9613516900000E-01
   1 -2.9613516900000E-01  1.5519489820000E+00  1.5519489820000E+00
   1 -1.5519489820000E+00 -1.5519489820000E+00 -2.9613516900000E-01
   1  2.9613516900000E-01  1.5519489820000E+00 -1.5519489820000E+00
   1  1.5519489820000E+00 -1.5519489820000E+00  2.9613516900000E-01
   1  2.9613516900000E-01 -1.5519489820000E+00  1.5519489820000E+00
   1 -1.5519489820000E+00  1.5519489820000E+00  2.9613516900000E-01
   1 -2.9613516900000E-01 -1.5519489820000E+00 -1.5519489820000E+00
 
C  0
       S    6 1.
  0.3047524880000E+04  0.1834737130000E-02
  0.4573695180000E+03  0.1403732280000E-01
  0.1039486850000E+03  0.6884262220000E-01
  0.2921015530000E+02  0.2321844430000E+00
  0.9286662960000E+01  0.4679413480000E+00
  0.3163926960000E+01  0.3623119850000E+00
       SP   3 1.
  0.7868272350000E+01 -0.1193324200000E+00  0.6899906660000E-01
  0.1881288540000E+01 -0.1608541520000E+00  0.3164239610000E+00
  0.5442492580000E+00  0.1143456440000E+01  0.7443082910000E+00
       SP   1 1.
  0.1687144782000E+00  0.1000000000000E+01  0.1000000000000E+01
       D    1 1.
  0.8000000000000E+00  0.1000000000000E+01
****
H  0
       S    3 1.
  0.1873113696000E+02  0.3349460434000E-01
  0.2825394365000E+01  0.2347269535000E+00
  0.6401216923000E+00  0.8137573262000E+00
       S    1 1.
  0.1612777588000E+00  0.1000000000000E+01
       P    1 1.
  0.1100000000000E+01  0.1000000000000E+01
****
 

Running these two calculations give you an energy difference of 0.0000003255398 Hartree.

So, turning the two codes into enough correspondence to trust the basis set conversion at the RHF/UHF level, IT IS REPORTED that one must include the following for CRYSTALXX:

BOHRANGS
0.529177249
... 
GAUSS98
... 
TOLINTEG
20 20 20 20 20
... 
NOBIPOLA
... 
TOLDEP
8 

Technically, the GAUSS98 keyword doesn’t gain you anything except a Gaussian-friendly coordinate file (but I include it here anyway).

Then do the following for Gaussian:

# 5D 7F

This brings your CRYSTALXX into correspondence with GaussianYY, not vice versa (re: B3LYP, cut-offs, etc.).

NOTE 5: DFT Calculations Are A Completely Different Matter

Density functional theory calculations are sensitive both to the proper specification of the density functional (see above for B3LYP) and the fineness of the grid (if you’re doing grid-based DFT). Unfortunately, there isn’t an exact correspondence between the grid specifications of the two programs (or the treatment of the grids in the two programs), which means there isn’t a way to exactly zero-out the differences between this part of the energy comparison for the two. I suppose one could attempt to run infinitely fine meshes to see what happens, but I’ve not seen it reported. That said, there’s enough correspondence in the different qualities of pre-defined grids to get you close enough to, again, wave off differences in the two energies to issues not related to the basis sets themselves.

This brings up a slightly off-topic point of discussion that hopefully will spare you a reviewer’s wrath. When a good journal reviewer sees someone report as their theoretical methods section:

Calculations were performed at the B3LYP/6-31G(d,p) level with the [insert program name] program.

… and nothing else, they become quite put off. There are several factors that will affect the ability of a future researcher to reproduce your data (if necessary). If not providing your input files, the bare minimum that should appear in a theory section includes:

* Electron correlation method (RHF, defined functional, MP2, etc.)
* A Reference To That Electron Correlation Method
* Basis Set
* A Reference To That Basis Set
* Convergence Criteria
* Grid Size for DFT calculations
* Version of the software
* A Reference To That Version of the software

… and if you’re just using program defaults (which is what is assumed when no other information is provided in the Methods Section), there’s no shame in stating that as well.

To beat on the issue of grid specification, here’s a plot of the energy of simple CH4 with varied Gaussian grid specifications (CRYSTAL09 showing a similar sensitivity to grid choice) (PPS = points per shell):

2014dec3_gaussianshells

You can see that, after a certain fineness, the calculations produce the same energies (the “infinitely fine” case for Gaussian in this case. Any finer mesh is overkill. This also shows WHY you need to specify your grid when reporting your results!). The grid, or the fineness of mesh, group into kind-of categories in Gaussian and CRYSTAL. To summarize briefly:

Gaussian Specifications:

Program Option “Coarse” – 35 radial shells and 110 angular points per shell (35,110)
Program Option “Fine” – (75,302)
Program Option “Ultrafine” – (99,590)

CRYSTAL Specifications:

Again, a few pre-defined grids are available.

Default (55,434)
Default grid - corresponds to the sequence:
RADIAL
1
4.0
55
ANGULAR
10
0.4 0.6 0.8 0.9 1.1 2.3 2.4 2.6 2.8 9999.0
1 2 5 8 11 13 11 8 5 1
Large (75,434)
RADIAL
1
4.0
75
ANGULAR
5
0.1667 0.5 0.9 3.05 9999.0
2 6 8 13 8
XLGRID (75,974)
RADIAL
1
4.0
75
ANGULAR
5
0.1667 0.5 0.9 3.5 9999.0
4 8 12 16 12
XXLGRID (99,1454)
RADIAL
1
4.0
99
ANGULAR
5
0.1667 0.5 0.9 3.5 9999.0
6 10 14 18 14

Which is all to be contrasted with the GAMESS-US approach of grid specification:

In GAMESS, you specify the components.

NRAD   = number of radial points in the Euler-MacLaurin                         
         quadrature. (96 is reasonable)                                         
                                                                                
NTHE   = number of angle theta grids in Gauss-Legendre                          
         quadrature (polar coordinates). (12 is reasonable)                     
                                                                                
NPHI   = number of angle phi grids in Gauss-Legendre                            
         quadrature.  NPHI should be double NTHE so points                      
         are spherically distributed. (24 is reasonable)                        
                                                                                
The number of angular points will be NTHE*NPHI.  The values                     
shown give a gradient accuracy near the default OPTTOL of                       
0.00010, while NTHE=24 NPHI=48 approaches OPTTOL=0.00001,                       
and "army grade" is NTHE=36 NPHI=72.                        

NOTE 6: EMSL vs. Built-In Gaussian Basis Sets

I am pleased to report there appears to be no difference running Gaussian with the built-in 6-31G(d,p) and using the EMSL Basis Set Exchange 6-31G(d,p) set (this fact was not obvious at the beginning of this test), but ONLY with the 5D and 7F keywords (specifying the number of angular momentum functions to use for the d and f shells) added (the EMSL basis sets will produce the same results either way. Gaussian’s behavior with its internal basis sets DOES change).

By that, I mean the following for Argon with the B3LYP and B5LYP (B3LYP alt.) functionals.

NOTE: Those lines with 5D 7F show identical energies for the B3LYP and B5LYP pairs. The others, not so much.

B3LYP
B3LYP
B5LYP
B5LYP
Internal 6-31G(d,p)
EMSL 6-31G(d,p)
Internal 6-31G(d,p)
EMSL 6-31G(d,p)
grid=coarse
-527.51705491
-527.51322582
-527.44745782
-527.44362696
grid=coarse, 5D 7F
-527.51322582
-527.51322582
-527.44362696
-527.44362696
grid=fine
-527.51714180
-527.51331287
-527.44754491
-527.44371422
grid=fine, 5D 7F
-527.51331287
-527.51331287
-527.44371422
-527.44371422
grid=ultrafine
-527.51714191
-527.51331298
-527.44754502
-527.44371433
grid=ultrafine, 5D 7F
-527.51331298
-527.51331298
-527.44371433
-527.44371433

NOTE 7: The Optimizers Affect The Final Energies

At the tail end of this energy comparison analysis came the identification of the quality of the optimization itself affecting the final energy differences. While the criteria for optimization in CRYSTALXX is very much like that in Gaussian as far as format is concerned, the reaching of an energetic minimum is different enough to produce energies differences of 10^-5 Hartree or more. My solution to this was to hammer on both the energy and geometry convergence criteria in CRYSTALXX, using:

TOLDEE (SCF and Optimization): 14
TOLDEG: 0.000001
TOLDEX: 0.000001

Nearly ridiculous convergence criteria and a massive waste of computing resources if you’re doing anything but trying to reproduce certain types of calculations (or if you’ve a molecule with +10 freely-rotatable but weakly interacting methyl groups). Your familiar-to-Gaussian-users convergence criteria will look like the following in CRYSTALXX:

 GRADIENT NORM     0.000001  GRADIENT THRESHOLD     0.500000

 MAX GRADIENT      0.000001  THRESHOLD              0.000002 CONVERGED YES
 RMS GRADIENT      0.000001  THRESHOLD              0.000001 CONVERGED YES
 MAX DISPLAC.      0.000000  THRESHOLD              0.000008 CONVERGED YES
 RMS DISPLAC.      0.000000  THRESHOLD              0.000005 CONVERGED YES

My practice with this phenomenon came from optimization attempts of Cl2 (one of the more difficult structures to get into agreement with the two codes early on). While Gaussian will generally take any number of starting geometries and produce the same result, CRYSTAL optimization is found to be very sensitive to the starting geometry, with closer initial Cl-Cl distances producing better agreements with Gaussian.

As a point of larger discussion, it is well known that one of Gaussian’s great benefits over several other codes is the quality of the convergers – you may not like the answer, but Gaussian is, generally, very good at finding minima. Where you have problems, you either have lots of keywords to adjust or lots of behind-the-curtain operations Gaussian does to attempt to find better geometries. Generally, CRYSTAL and Gaussian settled on the same structures. For some cases, the two disagreed on geometry, energy, or both when optimizing dimers (granted, the first row transition metals can be a tough block to make dimers out of), leaving one to “swap out” the optimized geometries from both programs to see if they, at least, agreed on the minimum from code A being an identifiable minimum in code B (which was generally, but not always, the case).

NOTE 8: Test(able) Structures And Assorted Convergence Problems

Finally, it should be stated that the energy analysis was performed to test if the basis sets were correctly converted, NOT to test the programs. I spent as much time as I thought reasonable on this analysis but ran into a few cases that tested my knowledge of keyword combinations and, more generally, tried my patience.

The test structures can be broken into three categories:

1. Full Shell (Noble and Noble-ish) Elements

That’s Ar, Be, Ca, He, Mg, Ne, and Zn.

2. Homodimers As Forced Singlets

That’s H2, Li2, B2, C2, N2, O2, F2, Na2, Al2, Si2, P2, S2, Cl2, K2, Sc2, Ti2, V2, Cr2, Mn2, Fe2, Co2, Ni2, and Cu2.

The dimers and singlets combination grew out of an early frustration when trying to get doublets to be well-behaved in CRYSTAL09. For instance, I could not get CRYSTAL09 to give me an UHF energy for the single Flourine doublet.

Dimers made several combinations easy (H2,F2,Cl2,N2,C2), one easier (Al2), and three less easy (O2,S2,B2). You say to yourself “O2 is a ground-state triplet. Why run the singlet?” My answer is “I didn’t want to deal with unpaired-ness as part of the survey (else would have run a bunch of doublets). And a singlet is a singlet (I thought), so the comparison for the sake of comparing energies is still valid.”

It should be obvious that dimerization in all of the non-full shell cases simplifies life by allowing you to always define a system with a RHF wavefunction (no unpaired electrons, even if they really, really want to be). This approximation in all cases has less to do with a lacking working knowledge of transition metals (but, hey, it has been a while) than it does with an interest in computational expediency. If CRYSTAL and Gaussian can be made to produce identical structures, I believe the basis set conversion even if I don’t believe the reasonability of the optimized structure (which is to say, I did spend significant time getting Gaussian and CRYSTAL to produce the same structure, but didn’t spend any time the best geometry from sets of optimizations).

3. Hydrides For Some Non-Ideal Homodimer Optimizations

That’s AlH3, BH3, CoH3, H2O, H2S, KH, MnH5, NaH, NiH2, VH3.

The production of energetic minima among transition metal homodimers is complicated in the two codes by the presence of multiple minima for these species (we’re talking lots of ways to combine electrons). O2 and S2 Hartree-Fock calculations proved to be annoyingly problematic despite several efforts. The energy difference between the low-spin (singlet) and high-spin (triplet) cases produced too-small numbers in CRYSTAL09 compared to Gaussian. Boron is just naturally poorly-behaved, Aluminum less so. Manganese and nickel were a serious fight to get RHF values to agree. Na2 and K2 weren’t bad, but I thought the agreement could get better (hence NaH and KH). Same for V2 (in the form of VH3).

For a selection of cases, the homodimers are reported (to show how badly they behave), but the appropriately valence-satisfied hydrides for these elements are also reported (where it is shown that the energies between CRYSTAL and Gaussian look great).

NOTE 9: What’s Good Enough?

As too much text above explains, getting CRYSTALXX and GaussianXX to agree to too many significant digits by DFT is more work than it’s worth. Getting Hartree-Fock (esp. RHF) to agree to within narrow tolerances is not a problem provided you really beat on the energy criteria and structure optimizations. A summary of the energy differences between Gaussian09 and CRYSTAL09 for RHF and “best case” DFT are provided below. RHF is my guide here to prove that the basis set conversion was successful. The DFT results show how “very high quality” Gaussian09 and “very high quality” CRYSTAL09 still differ in their final energies.

Atom, Molecule
Best Keyword
RHF Difference
With 6-31G(d,p)
Best Keyword Match
DFT Difference
With 6-31G(d,p)
Notes
Al2
0.0000000959
-0.0000021180
Difference Per Atom
AlH3
0.0000000044
-0.0001532824
Hydride Alternative Optmization
Ar
0.0000000000
0.0000079653
Single atom
B2
0.0160814822
-0.0119799981
Difference Per Atom
BH3
0.0000000002
-0.0000043200
Hydride Alternative Optmization
Be
0.0000000000
-0.0000015870
Single atom
C2
0.0000000385
-0.0000230890
Difference Per Atom
Ca
0.0000000003
0.0000134887
Single atom
Cl2
0.0000000945
-0.0000013374
Difference Per Atom
Co2
0.0004687257
-0.0000485513
Difference Per Atom
CoH3
0.0000000269
-0.0003096507
Hydride Alternative Optmization
Cr2
-0.0000001317
-0.0000701267
Difference Per Atom
Cu2
-0.0000043954
0.0000462382
Difference Per Atom
F2
0.0000000586
0.0000000730
Difference Per Atom
Fe2
0.0000001773
-0.0000175537
Difference Per Atom
H2
0.0000000025
0.0000000010
Difference Per Atom
He
0.0000000000
0.0000000000
Single atom
K2
-0.0000019804
-0.0010458054
Difference Per Atom
KH
-0.0000000021
-0.0000958239
Hydride Alternative Optmization
Li2
0.0000000001
-0.0006904112
Difference Per Atom
Mg
-0.0000000003
-0.0000009333
Single atom
Mn2
-0.0002591557
-0.0554301772
Difference Per Atom
MnH5
0.0000000241
0.0000023412
Hydride Alternative Optmization
N2
0.0000000098
-0.0000055645
Difference Per Atom
Na2
-0.0000001262
-0.0003885180
Difference Per Atom
NaH
-0.0000000007
-0.0000262128
Hydride Alternative Optmization
Ne
0.0000000003
-0.0000007236
Single atom
Ni2
-0.0000101151
-0.0020160551
Difference Per Atom
NiH2
0.0000000050
-0.0000066828
Hydride Alternative Optmization
O2
0.2506265617
-0.0353640801
Difference Per Atom
H2O
0.0000000004
0.0000010523
Hydride Alternative Optmization
P2
-0.0000000409
-0.0006573436
Difference Per Atom
S2
0.1401697163
-0.0174734608
Difference Per Atom
H2S
0.0000000072
-0.0002853645
Hydride Alternative Optmization
Sc2
0.0000002473
-0.0000234407
Difference Per Atom
Si2
-0.0000000110
-0.0000390207
Difference Per Atom
Ti2
0.0000005480
-0.0000421595
Difference Per Atom
V2
-0.0757905400
-0.0000554233
Difference Per Atom
VH3
0.0000000100
–0.0000089300
Hydride Alternative Optmization
Zn
-0.0000000034
-0.0000013193
Single atom

NOTE 10: Keywords

As discussed in NOTE 4 above, you need to specify several parameters to make Gaussian and CRYSTAL agree. In the interest of complete overkill, I decided I wanted to know how the keyword combinations change the final energies from the runs. To that end, the summarized energies from all of the runs performed for the analysis is a bit exhaustive and full of lots of identical data (which is a good thing). These keywords are summarized below.

Parse The RHF Calculations As Follows:

H2__rhf__631Gdp__BOHRANGS__NOBIPOLA__10sTOLINTEG__TOLDEP__GAUSS98

As is a habit, all of the files are named with the relevant keyword combinations in the filenames themselves for ease of sorting.

H2
rhf
631Gdp
BOHRANGS
NOBIPOLA
10sTOLINTEG
TOLDEP
GAUSS98

Additional for the DFT calculations:

DefGRID__BOHRANGS__NOBIPOLA__20sTOLINTEG__TOLDEP__GAUSS98

Differ by the specification of the grid.

DefGRID
LGRID
XLGRID
XXLGRID

You will note that, very generally, the same energies are produced for many of the varied keyword combinations. That said, some difference throughout exist. I will not dwell on the differences here (well, only slightly), only remark that keyword choices affect final energies when trying to perform program comparisons, and differences in keywords may alter relative energies when using two different input files for the same structure. As you might expect, when in doubt, use identical keyword sets.

Just to explain what’s going on in each Excel tab (Excel file can be downloaded at the link at the bottom of this post), here’s a colorized sample case for H2.

2014nov30_testinglabels

* RED Set – RHF CRYSTAL runs with varied keyword combinations (filenames and energies)

* GREEN Set – RHF Gaussian09 runs with, in order, the internal basis set, internal + 5D 7F, EMSL basis set, and EMSL basis set + 5D 7F

* RED and GREEN bordered – the energies compared for the relative energies of the two programs.

* Gaussian – CRYSTAL Difference Using Boxed Values – Should be Obvious

* Difference Per Atom Using Boxed Values – For the homodimers, the difference divided by 2

* BLUE Set – CRYSTAL09 B3LYP/6-31G(d,p) Energies with difference keyword sets

* BLUE Background – Gaussian09’s B3LYP/6-31G(d,p) calculations with the internal 6-31G(d,p) Basis Set

* YELLOW Background – Gaussian09’s B3LYP/6-31G(d,p) calculations with the EMSL 6-31G(d,p) Basis Set

* ORANGE Set – Gaussian Alternative B3LYP/6-31G(d,p) (B5LYP) calculations with the internal 6-31G(d,p) Basis Set

* BLACK Set – Gaussian Alternative B3LYP/6-31G(d,p) (B5LYP) calculations with the EMSL 6-31G(d,p) Basis Set

* Gaussian-CRYSTAL Difference – The B3LYP/6-31G(d,p) Energy Differences For the “B5LYP” EMSL 6-31G(d,p) Cases (best comparisons). The bordered CRYSTAL09 keyword set (XLGRID__NOBIPOLA__20sTOLINTEG__TOLDEP__GAUSS98) is used.

* LIGHT GREEN Background – These calculations don’t include the GAUSS98 keyword, which only produces a formatted GAUSSIAN.DAT file. You’d think the presence of absence of this keyword would mean nothing, so I consider this a control case for keyword sensitivity.

NOTE 11: Some Lessons Learned (Briefly) From Some Small Systems

1. CRYSTAL is much more sensitive to the starting geometry than Gaussian when it comes to finding a stable minimum. Simply changing an interatomic distance by a tenth of an Angstrom is enough to cause a failed optimization to work (and vice versa).

2. Generally, both programs settle on the same minimum. This is easy when the systems are well-behaved (hence the hydrides). For several of the metal systems, the two programs consistently disagreed on the minimum energy geometry (which is not unexpected in some ways).

3. DFT vs. RHF and the addition of END – You might assume that the replacement of B3LYP with RHF in a CRYSTAL input file would look something like:

B3LYP
END

RHF
END

You would, in fact, be wrong. Including this END statement for RHF reads as a hard END for the program. I spent far too long wondering why all of my parameters were being ignored in the RHF runs until I happened to delete the END after RHF, after which life became much simpler. Careful with your calls!

4. CRYSTAL can produce multiple minima for the same starting geometry with different keyword choices. This is not too surprising, as many keyword combinations can interact to result in different early sampling of forces and energies. That said, this is also shown to be element-specific. In the Excel file, Tabs with a “-” at the beginning contain RHF results that show differences (10ths to 1000ths of Hartrees) among the various RHF keyword choices. NiH2 6-31G optimizations, as just one example, group into two structures with a 0.46 Hartree difference in energy that differ by Ni-H bond lengths of 0.006 Angstroms.

For those causally reading, 0.46 Hartree is about 1207 kJ/mol, which is a completely insane amount. This is true, but the program terminated normally. Sadly, normal mode analyses failed for both cases with the same keyword sets (no additional modification to get things to normal mode properly) and, because my concern was only testing the energies to confirm that the basis sets were properly converted, I have not pursued any of these problem cases further.

Can this energy difference issue in the RHF series be dealt with? Certainly. Swapping geometries from one optimization into another input file with… conflicting keyword sets will often produce the original geometry. That said, if you were simply going into the optimizations with these small structures and did not know you were facing the possibility of local minima around a global minimum, you’d risk missing the ridiculous 0.46 Hartree of energy.

The RHF optimization variations in keyword combinations for Co2 6-31G and 6-31G(d,p), Ni2 6-31G and 6-31G(d,p), and NiH2 6-31G and 6-31G(d,p) are marked accordingly. Academically interesting but not pursued further.

5. Boron, Oxygen, Sulfur, Vanadium – Vanadium was far and away the worst dimer to deal with in RHF calculations, to the point where this post would have gone up a week sooner had it been more well-behaved. While the hydride (VH3) is well behaved, V2 settles on one of two minima and CRYSTAL and Gaussian seem to have a very difficult time deciding what that minimum is. One optimization attempt produced a CRYSTAL result consistent with Gaussian, while all others produced an alternative minimum (with the difference obvious in the bond lengths).

My goal in the analysis was NOT to employ multiple convergence keywords/tools to force structures into agreement, as I wanted to find out what different keyword combinations did to affect the final energies and geometries. I suspect B2, O2, S2, and V2 could be made to agree between CRYSTAL and Gaussian. That said, efforts with ONLY the keyword sets used for all of the other comparisons in the element series reveal that CRYSTAL and Gaussian differ in the optimized geometries for these four cases in ways that they do not differ for any other element sets.

Performing the same calculations on the hydrides produces excellent agreement between the two codes (and are my tests to believe that the basis set conversion was successful). Worse still (at least for the continuity of the RHF-centric presentation above), the V2 DFT energies between CRYSTAL and Gaussian are nearly identical (among the best for the larger elements) while the RHF values are far from agreement despite several geometry-swapping attempts (CRYSTAL and Gaussian see two different electronic states and see starting geometries as higher-energy versions of those two different states. A tricky problem to tackle generally).




And, Finally…

The Files

The 6-31G Basis Sets can be downloaded here: 2014dec30_631G_CRYSTAL_Basis_Sets.txt

The 6-31G(d) Basis Sets can be downloaded here: 2014dec30_631Gd_CRYSTAL_Basis_Sets.txt

The 6-31G(d,p) Basis Sets can be downloaded here: 2014dec30_631Gdp_CRYSTAL_Basis_Sets.txt

For those wanting to perform their own tests, all of the input and output files from ALL of the runs are provided here (55 MB zip file): 2014dec30_Crystal_Basis_Sets_Run_Files.zip

For those who want to see the numbers for all of the tests, the excel file containing all of the data can be downloaded here: 2014dec30_Crystal_Basis_Sets_Run_results.xlsx.zip


The 6-31G Gaussian-Type Basis Sets

In order and in CRYSTAL format below. For those wondering, you generate the 6-31G set by taking the extra group of coefficients off the back-end of the 6-31G(d,p) basis sets. Compare any element from the two groups and you’ll see the difference.

NOTE: If making similar modifications to other basis sets with added polarization or diffuse functions, you need to change the number of shells after the element in the first row of each element when you delete the bottom shell (so, for H, “1 3” for 6-31G(d,p) becomes “1 2” for 6-31G. If you’ve a problem with a CRYSTAL run with a home-converted basis set, check that first).

1  2      
0 0 3 1.0 1.0
  1.8731136960E+01   3.3494604340E-02    
  2.8253943650E+00   2.3472695350E-01    
  6.4012169230E-01   8.1375732620E-01    
0 0 1 0.0 1.0
  1.6127775880E-01   1.0000000000E+00    

2  2    
0 0 3 2.0 1.0
  3.8421634000E+01   2.3766000000E-02
  5.7780300000E+00   1.5467900000E-01
  1.2417740000E+00   4.6963000000E-01
0 0 1 0.0 1.0
  2.9796400000E-01   1.0000000000E+00
  
3  3      
0 0 6 2.0 1.0
  6.4241892000E+02   2.1426000000E-03
  9.6798515000E+01   1.6208900000E-02
  2.2091121000E+01   7.7315600000E-02
  6.2010703000E+00   2.4578600000E-01
  1.9351177000E+00   4.7018900000E-01
  6.3673580000E-01   3.4547080000E-01
0 1 3 1.0 1.0
  2.3249184000E+00  -3.5091700000E-02   8.9415000000E-03
  6.3243060000E-01  -1.9123280000E-01   1.4100950000E-01
  7.9053400000E-02   1.0839878000E+00   9.4536370000E-01
0 1 1 0.0 1.0
  3.5962000000E-02   1.0000000000E+00   1.0000000000E+00

4  3      
0 0 6 2.0 1.0
  1.2645857000E+03   1.9448000000E-03
  1.8993681000E+02   1.4835100000E-02
  4.3159089000E+01   7.2090600000E-02
  1.2098663000E+01   2.3715420000E-01
  3.8063232000E+00   4.6919870000E-01
  1.2728903000E+00   3.5652020000E-01
0 1 3 2.0 1.0
  3.1964631000E+00  -1.1264870000E-01   5.5980200000E-02
  7.4781330000E-01  -2.2950640000E-01   2.6155060000E-01
  2.1996630000E-01   1.1869167000E+00   7.9397230000E-01
0 1 1 0.0 1.0
  8.2309900000E-02   1.0000000000E+00   1.0000000000E+00

5  3      
0 0 6 2.0 1.0
  2.0688823000E+03   1.8663000000E-03
  3.1064957000E+02   1.4251500000E-02
  7.0683033000E+01   6.9551600000E-02
  1.9861080000E+01   2.3257290000E-01
  6.2993048000E+00   4.6707870000E-01
  2.1270270000E+00   3.6343140000E-01
0 1 3 3.0 1.0
  4.7279710000E+00  -1.3039380000E-01   7.4597600000E-02
  1.1903377000E+00  -1.3078890000E-01   3.0784670000E-01
  3.5941170000E-01   1.1309444000E+00   7.4345680000E-01
0 1 1 0.0 1.0
  1.2675120000E-01   1.0000000000E+00   1.0000000000E+00

6  3      
0 0 6 2.0 1.0
  3.0475248800E+03   1.8347371300E-03    
  4.5736951800E+02   1.4037322800E-02    
  1.0394868500E+02   6.8842622200E-02    
  2.9210155300E+01   2.3218444300E-01    
  9.2866629600E+00   4.6794134800E-01    
  3.1639269600E+00   3.6231198500E-01    
0 1 3 4.0 1.0
  7.8682723500E+00  -1.1933242000E-01   6.8999066600E-02  
  1.8812885400E+00  -1.6085415200E-01   3.1642396100E-01  
  5.4424925800E-01   1.1434564400E+00   7.4430829100E-01  
0 1 1 0.0 1.0
  1.6871447820E-01   1.0000000000E+00   1.0000000000E+00  

7  3      
0 0 6 2.0 1.0
  4.1735110000E+03   1.8348000000E-03    
  6.2745790000E+02   1.3995000000E-02    
  1.4290210000E+02   6.8587000000E-02    
  4.0234330000E+01   2.3224100000E-01    
  1.2820210000E+01   4.6907000000E-01    
  4.3904370000E+00   3.6045500000E-01    
0 1 3 5.0 1.0
  1.1626358000E+01  -1.1496100000E-01   6.7580000000E-02  
  2.7162800000E+00  -1.6911800000E-01   3.2390700000E-01  
  7.7221800000E-01   1.1458520000E+00   7.4089500000E-01  
0 1 1 0.0 1.0
  2.1203130000E-01   1.0000000000E+00   1.0000000000E+00  

8  3      
0 0 6 2.0 1.0
  5.4846717000E+03   1.8311000000E-03    
  8.2523495000E+02   1.3950100000E-02    
  1.8804696000E+02   6.8445100000E-02    
  5.2964500000E+01   2.3271430000E-01    
  1.6897570000E+01   4.7019300000E-01    
  5.7996353000E+00   3.5852090000E-01    
0 1 3 6.0 1.0
  1.5539616000E+01  -1.1077750000E-01   7.0874300000E-02  
  3.5999336000E+00  -1.4802630000E-01   3.3975280000E-01  
  1.0137618000E+00   1.1307670000E+00   7.2715860000E-01  
0 1 1 0.0 1.0
  2.7000580000E-01   1.0000000000E+00   1.0000000000E+00  

9  3      
0 0 6 2.0 1.0
  7.0017130900E+03   1.8196169000E-03
  1.0513660900E+03   1.3916079600E-02
  2.3928569000E+02   6.8405324500E-02
  6.7397445300E+01   2.3318576000E-01
  2.1519957300E+01   4.7126743900E-01
  7.4031013000E+00   3.5661854600E-01
0 1 3 7.0 1.0
  2.0847952800E+01  -1.0850697500E-01   7.1628724300E-02
  4.8083083400E+00  -1.4645165800E-01   3.4591210300E-01
  1.3440698600E+00   1.1286885800E+00   7.2246995700E-01
0 1 1 0.0 1.0
  3.5815139300E-01   1.0000000000E+00   1.0000000000E+00

10  3    
0 0 6 2.0 1.0
  8.4258515300E+03   1.8843481000E-03
  1.2685194000E+03   1.4336899400E-02
  2.8962141400E+02   7.0109623300E-02
  8.1859004000E+01   2.3737326600E-01
  2.6251507900E+01   4.7300712600E-01
  9.0947205100E+00   3.4840124100E-01
0 1 3 8.0 1.0
  2.6532131000E+01  -1.0711828700E-01   7.1909588500E-02
  6.1017550100E+00  -1.4616382100E-01   3.4951337200E-01
  1.6962715300E+00   1.1277735000E+00   7.1994051200E-01
0 1 1 0.0 1.0
  4.4581870000E-01   1.0000000000E+00   1.0000000000E+00

11  4
0 0 6 2.0 1.0
  9.9932000000E+03   1.9377000000E-03
  1.4998900000E+03   1.4807000000E-02
  3.4195100000E+02   7.2706000000E-02
  9.4679700000E+01   2.5262900000E-01
  2.9734500000E+01   4.9324200000E-01
  1.0006300000E+01   3.1316900000E-01
0 1 6 8.0 1.0
  1.5096300000E+02  -3.5421000000E-03   5.0017000000E-03      
  3.5587800000E+01  -4.3959000000E-02   3.5511000000E-02      
  1.1168300000E+01  -1.0975210000E-01   1.4282500000E-01      
  3.9020100000E+00   1.8739800000E-01   3.3862000000E-01      
  1.3817700000E+00   6.4669900000E-01   4.5157900000E-01      
  4.6638200000E-01   3.0605800000E-01   2.7327100000E-01      
0 1 3 1.0 1.0
  4.9796600000E-01  -2.4850300000E-01  -2.3023000000E-02      
  8.4353000000E-02  -1.3170400000E-01   9.5035900000E-01      
  6.6635000000E-02   1.2335200000E+00   5.9858000000E-02      
0 1 1 0.0 1.0
  2.5954400000E-02   1.0000000000E+00   1.0000000000E+00      

12  4 
0 0 6 2.0 1.0
  1.1722800000E+04   1.9778000000E-03         
  1.7599300000E+03   1.5114000000E-02         
  4.0084600000E+02   7.3911000000E-02         
  1.1280700000E+02   2.4919100000E-01         
  3.5999700000E+01   4.8792800000E-01         
  1.2182800000E+01   3.1966200000E-01         
0 1 6 8.0 1.0
  1.8918000000E+02  -3.2372000000E-03   4.9281000000E-03      
  4.5211900000E+01  -4.1008000000E-02   3.4989000000E-02      
  1.4356300000E+01  -1.1260000000E-01   1.4072500000E-01      
  5.1388600000E+00   1.4863300000E-01   3.3364200000E-01      
  1.9065200000E+00   6.1649700000E-01   4.4494000000E-01      
  7.0588700000E-01   3.6482900000E-01   2.6925400000E-01      
0 1 3 2.0 1.0
  9.2934000000E-01  -2.1229000000E-01  -2.2419000000E-02      
  2.6903500000E-01  -1.0798500000E-01   1.9227000000E-01      
  1.1737900000E-01   1.1758400000E+00   8.4618100000E-01      
0 1 1 0.0 1.0
  4.2106100000E-02   1.0000000000E+00   1.0000000000E+00      
  
13  4
0 0 6 2.0 1.0
  1.3983100000E+04   1.9426700000E-03         
  2.0987500000E+03   1.4859900000E-02         
  4.7770500000E+02   7.2849400000E-02         
  1.3436000000E+02   2.4683000000E-01         
  4.2870900000E+01   4.8725800000E-01         
  1.4518900000E+01   3.2349600000E-01         
0 1 6 8.0 1.0
  2.3966800000E+02  -2.9261900000E-03   4.6028500000E-03      
  5.7441900000E+01  -3.7408000000E-02   3.3199000000E-02      
  1.8285900000E+01  -1.1448700000E-01   1.3628200000E-01      
  6.5991400000E+00   1.1563500000E-01   3.3047600000E-01      
  2.4904900000E+00   6.1259500000E-01   4.4914600000E-01      
  9.4454000000E-01   3.9379900000E-01   2.6570400000E-01      
0 1 3 3.0 1.0
  1.2779000000E+00  -2.2760600000E-01  -1.7513000000E-02      
  3.9759000000E-01   1.4458300000E-03   2.4453300000E-01      
  1.6009500000E-01   1.0927900000E+00   8.0493400000E-01      
0 1 1 0.0 1.0
  5.5657700000E-02   1.0000000000E+00   1.0000000000E+00      
  
14  4
0 0 6 2.0 1.0
  1.6115900000E+04   1.9594800000E-03         
  2.4255800000E+03   1.4928800000E-02         
  5.5386700000E+02   7.2847800000E-02         
  1.5634000000E+02   2.4613000000E-01         
  5.0068300000E+01   4.8591400000E-01         
  1.7017800000E+01   3.2500200000E-01         
0 1 6 8.0 1.0
  2.9271800000E+02  -2.7809400000E-03   4.4382600000E-03      
  6.9873100000E+01  -3.5714600000E-02   3.2667900000E-02      
  2.2336300000E+01  -1.1498500000E-01   1.3472100000E-01      
  8.1503900000E+00   9.3563400000E-02   3.2867800000E-01      
  3.1345800000E+00   6.0301700000E-01   4.4964000000E-01      
  1.2254300000E+00   4.1895900000E-01   2.6137200000E-01      
0 1 3 4.0 1.0
  1.7273800000E+00  -2.4463000000E-01  -1.7795100000E-02      
  5.7292200000E-01   4.3157200000E-03   2.5353900000E-01      
  2.2219200000E-01   1.0981800000E+00   8.0066900000E-01      
0 1 1 0.0 1.0
  7.7836900000E-02   1.0000000000E+00   1.0000000000E+00      

15  4
0 0 6 2.0 1.0
  1.9413300000E+04   1.8516000000E-03         
  2.9094200000E+03   1.4206200000E-02         
  6.6136400000E+02   6.9999500000E-02         
  1.8575900000E+02   2.4007900000E-01         
  5.9194300000E+01   4.8476200000E-01         
  2.0031000000E+01   3.3520000000E-01         
0 1 6 8.0 1.0
  3.3947800000E+02  -2.7821700000E-03   4.5646200000E-03      
  8.1010100000E+01  -3.6049900000E-02   3.3693600000E-02      
  2.5878000000E+01  -1.1663100000E-01   1.3975500000E-01      
  9.4522100000E+00   9.6832800000E-02   3.3936200000E-01      
  3.6656600000E+00   6.1441800000E-01   4.5092100000E-01      
  1.4674600000E+00   4.0379800000E-01   2.3858600000E-01      
0 1 3 5.0 1.0
  2.1562300000E+00  -2.5292300000E-01  -1.7765300000E-02      
  7.4899700000E-01   3.2851700000E-02   2.7405800000E-01      
  2.8314500000E-01   1.0812500000E+00   7.8542100000E-01      
0 1 1 0.0 1.0
  9.9831700000E-02   1.0000000000E+00   1.0000000000E+00      
  
16  4
0 0 6 2.0 1.0
  2.1917100000E+04   1.8690000000E-03         
  3.3014900000E+03   1.4230000000E-02         
  7.5414600000E+02   6.9696000000E-02         
  2.1271100000E+02   2.3848700000E-01         
  6.7989600000E+01   4.8330700000E-01         
  2.3051500000E+01   3.3807400000E-01         
0 1 6 8.0 1.0
  4.2373500000E+02  -2.3767000000E-03   4.0610000000E-03      
  1.0071000000E+02  -3.1693000000E-02   3.0681000000E-02      
  3.2159900000E+01  -1.1331700000E-01   1.3045200000E-01      
  1.1807900000E+01   5.6090000000E-02   3.2720500000E-01      
  4.6311000000E+00   5.9225500000E-01   4.5285100000E-01      
  1.8702500000E+00   4.5500600000E-01   2.5604200000E-01      
0 1 3 6.0 1.0
  2.6158400000E+00  -2.5037400000E-01  -1.4511000000E-02      
  9.2216700000E-01   6.6957000000E-02   3.1026300000E-01      
  3.4128700000E-01   1.0545100000E+00   7.5448300000E-01      
0 1 1 0.0 1.0
  1.1716700000E-01   1.0000000000E+00   1.0000000000E+00      

17  4
0 0 6 2.0 1.0
  2.5180100000E+04   1.8330000000E-03         
  3.7803500000E+03   1.4034000000E-02         
  8.6047400000E+02   6.9097000000E-02         
  2.4214500000E+02   2.3745200000E-01         
  7.7334900000E+01   4.8303400000E-01         
  2.6247000000E+01   3.3985600000E-01         
0 1 6 8.0 1.0
  4.9176500000E+02  -2.2974000000E-03   3.9894000000E-03      
  1.1698400000E+02  -3.0714000000E-02   3.0318000000E-02      
  3.7415300000E+01  -1.1252800000E-01   1.2988000000E-01      
  1.3783400000E+01   4.5016000000E-02   3.2795100000E-01      
  5.4521500000E+00   5.8935300000E-01   4.5352700000E-01      
  2.2258800000E+00   4.6520600000E-01   2.5215400000E-01      
0 1 3 7.0 1.0
  3.1864900000E+00  -2.5183000000E-01  -1.4299000000E-02      
  1.1442700000E+00   6.1589000000E-02   3.2357200000E-01      
  4.2037700000E-01   1.0601800000E+00   7.4350700000E-01      
0 1 1 0.0 1.0
  1.4265700000E-01   1.0000000000E+00   1.0000000000E+00      
  
18  4
0 0 6 2.0 1.0
  2.8348300000E+04   1.8252600000E-03         
  4.2576200000E+03   1.3968600000E-02         
  9.6985700000E+02   6.8707300000E-02         
  2.7326300000E+02   2.3620400000E-01         
  8.7369500000E+01   4.8221400000E-01         
  2.9686700000E+01   3.4204300000E-01         
0 1 6 8.0 1.0
  5.7589100000E+02  -2.1597200000E-03   3.8066500000E-03      
  1.3681600000E+02  -2.9077500000E-02   2.9230500000E-02      
  4.3809800000E+01  -1.1082700000E-01   1.2646700000E-01      
  1.6209400000E+01   2.7699900000E-02   3.2351000000E-01      
  6.4608400000E+00   5.7761300000E-01   4.5489600000E-01      
  2.6511400000E+00   4.8868800000E-01   2.5663000000E-01      
0 1 3 8.0 1.0
  3.8602800000E+00  -2.5559200000E-01  -1.5919700000E-02      
  1.4137300000E+00   3.7806600000E-02   3.2464600000E-01      
  5.1664600000E-01   1.0805600000E+00   7.4399000000E-01      
0 1 1 0.0 1.0
  1.7388800000E-01   1.0000000000E+00   1.0000000000E+00      

19  5
0 0 6 2.0 1.0
  3.1594420000E+04   1.8280100000E-03         
  4.7443300000E+03   1.3994030000E-02         
  1.0804190000E+03   6.8871290000E-02         
  3.0423380000E+02   2.3697600000E-01         
  9.7245860000E+01   4.8290400000E-01         
  3.3024950000E+01   3.4047950000E-01         
0 1 6 8.0 1.0
  6.2276250000E+02  -2.5029760000E-03   4.0946370000E-03      
  1.4788390000E+02  -3.3155500000E-02   3.1451990000E-02      
  4.7327350000E+01  -1.2263870000E-01   1.3515580000E-01      
  1.7514950000E+01   5.3536430000E-02   3.3905000000E-01      
  6.9227220000E+00   6.1938600000E-01   4.6294550000E-01      
  2.7682770000E+00   4.3458780000E-01   2.2426380000E-01      
0 1 6 8.0 1.0
  1.1848020000E+01   1.2776890000E-02  -1.2213770000E-02      
  4.0792110000E+00   2.0987670000E-01  -6.9005370000E-03      
  1.7634810000E+00  -3.0952740000E-03   2.0074660000E-01      
  7.8892700000E-01  -5.5938840000E-01   4.2813320000E-01      
  3.5038700000E-01  -5.1347600000E-01   3.9701560000E-01      
  1.4634400000E-01  -6.5980350000E-02   1.1047180000E-01      
0 1 3 1.0 1.0
  7.1680100000E-01  -5.2377720000E-02   3.1643000000E-02      
  2.3374100000E-01  -2.7985030000E-01  -4.0461600000E-02      
  3.8675000000E-02   1.1415470000E+00   1.0120290000E+00      
0 1 1 0.0 1.0
  1.6521000000E-02   1.0000000000E+00   1.0000000000E+00      
  
20  5
0 0 6 2.0 1.0
  3.5264860000E+04   1.8135010000E-03         
  5.2955030000E+03   1.3884930000E-02         
  1.2060200000E+03   6.8361620000E-02         
  3.3968390000E+02   2.3561880000E-01         
  1.0862640000E+02   4.8206390000E-01         
  3.6921030000E+01   3.4298190000E-01         
0 1 6 8.0 1.0
  7.0630960000E+02   2.4482250000E-03   4.0203710000E-03      
  1.6781870000E+02   3.2415040000E-02   3.1006010000E-02      
  5.3825580000E+01   1.2262190000E-01   1.3372790000E-01      
  2.0016380000E+01  -4.3169650000E-02   3.3679830000E-01      
  7.9702790000E+00  -6.1269950000E-01   4.6312810000E-01      
  3.2120590000E+00  -4.4875400000E-01   2.2575320000E-01      
0 1 6 8.0 1.0
  1.4195180000E+01   1.0845000000E-02  -1.2896210000E-02      
  4.8808280000E+00   2.0883330000E-01  -1.0251980000E-02      
  2.1603900000E+00   3.1503380000E-02   1.9597810000E-01      
  9.8789900000E-01  -5.5265180000E-01   4.3579330000E-01      
  4.4951700000E-01  -5.4379970000E-01   3.9964520000E-01      
  1.8738700000E-01  -6.6693420000E-02   9.7136360000E-02      
0 1 3 1.0 1.0
  1.0322710000E+00  -4.4397200000E-02  -4.2986210000E-01      
  3.8117100000E-01  -3.2845630000E-01   6.9358290000E-03      
  6.5131000000E-02   1.1630100000E+00   9.7059330000E-01      
0 1 1 0.0 1.0
  2.6010000000E-02   1.0000000000E+00   1.0000000000E+00      

21  7
0 0 6 2.0 1.00
  3.9088980000E+04   1.8032630000E-03   
  5.8697920000E+03   1.3807690000E-02   
  1.3369100000E+03   6.8003960000E-02   
  3.7660310000E+02   2.3470990000E-01   
  1.2046790000E+02   4.8156900000E-01   
  4.0980320000E+01   3.4456520000E-01   
0 1 6 8.0 1.0
  7.8628520000E+02   2.4518630000E-03   4.0395300000E-03
  1.8688700000E+02   3.2595790000E-02   3.1225700000E-02
  6.0009350000E+01   1.2382420000E-01   1.3498330000E-01
  2.2258830000E+01  -4.3598900000E-02   3.4247930000E-01
  8.8851490000E+00  -6.1771810000E-01   4.6231130000E-01
  3.6092110000E+00  -4.4328230000E-01   2.1775240000E-01
0 1 6 8.0 1.0
  2.9843550000E+01  -2.5863020000E-03  -6.0966520000E-03
  9.5423830000E+00   7.1884240000E-02  -2.6288840000E-02
  4.0567900000E+00   2.5032600000E-01   5.0910010000E-02
  1.7047030000E+00  -2.9910030000E-01   3.7980970000E-01
  7.0623400000E-01  -7.4468180000E-01   5.1708830000E-01
  2.7953600000E-01  -1.7997760000E-01   1.8297720000E-01
0 1 3 2.0 1.0
  1.0656090000E+00   6.4829780000E-02  -2.9384400000E-01
  4.2593300000E-01   3.2537560000E-01   9.2353230000E-02
  7.6320000000E-02  -1.1708060000E+00   9.8479300000E-01
0 1 1 0.0 1.0
  2.9594000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 1.0 1.0
  1.1147010000E+01   8.7476720000E-02   
  2.8210430000E+00   3.7956350000E-01   
  8.1962000000E-01   7.1803930000E-01   
0 3 1 0.0 1.0
  2.2146800000E-01   1.0000000000E+00   

22  7  
0 0 6 2.0 1.00
  4.3152950000E+04   1.7918720000E-03   
  6.4795710000E+03   1.3723920000E-02   
  1.4756750000E+03   6.7628300000E-02   
  4.1569910000E+02   2.3376420000E-01   
  1.3300060000E+02   4.8106960000E-01   
  4.5272220000E+01   3.4622800000E-01   
0 1 6 8.0 1.0   
  8.7468260000E+02   2.4310080000E-03   4.0176790000E-03
  2.0797850000E+02   3.2330270000E-02   3.1139660000E-02
  6.6879180000E+01   1.2425200000E-01   1.3490770000E-01
  2.4873470000E+01  -3.9039050000E-02   3.4316720000E-01
  9.9684410000E+00  -6.1717890000E-01   4.6257600000E-01
  4.0638260000E+00  -4.4730970000E-01   2.1546030000E-01
0 1 6 8.0 1.0   
  3.3643630000E+01  -2.9403580000E-03  -6.3116200000E-03
  1.0875650000E+01   7.1631030000E-02  -2.6976380000E-02
  4.6282250000E+00   2.5289150000E-01   5.3168470000E-02
  1.9501260000E+00  -2.9664010000E-01   3.8455490000E-01
  8.0945200000E-01  -7.4322150000E-01   5.1276620000E-01
  3.2047400000E-01  -1.8535200000E-01   1.8111350000E-01
0 1 3 2.0 1.0   
  1.2241480000E+00   6.3514650000E-02  -2.1120700000E-01
  4.8426300000E-01   3.1514040000E-01   7.7719980000E-02
  8.4096000000E-02  -1.1625950000E+00   9.8982140000E-01
0 1 1 0.0 1.0   
  3.2036000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 2.0 1.0   
  1.3690850000E+01   8.5894180000E-02   
  3.5131540000E+00   3.7846710000E-01   
  1.0404340000E+00   7.1612390000E-01   
0 3 1 0.0 1.0   
  2.8696200000E-01   1.0000000000E+00   

23  7
0 0 6 2.0 1.00   
  4.7354330000E+04   1.7845130000E-03   
  7.1107870000E+03   1.3667540000E-02   
  1.6195910000E+03   6.7361220000E-02   
  4.5633790000E+02   2.3305520000E-01   
  1.4606060000E+02   4.8063160000E-01   
  4.9757910000E+01   3.4748020000E-01   
0 1 6 8.0 1.0   
  9.6814840000E+02   2.4105990000E-03   3.9950050000E-03
  2.3028210000E+02   3.2072430000E-02   3.1040610000E-02
  7.4145910000E+01   1.2459420000E-01   1.3477470000E-01
  2.7641070000E+01  -3.4821770000E-02   3.4372790000E-01
  1.1114750000E+01  -6.1673740000E-01   4.6287590000E-01
  4.5431130000E+00  -4.5098440000E-01   2.1355470000E-01
0 1 6 8.0 1.0   
  3.7640500000E+01  -3.2331990000E-03  -6.4940560000E-03
  1.2282380000E+01   7.1307440000E-02  -2.7534530000E-02
  5.2333660000E+00   2.5438200000E-01   5.5162840000E-02
  2.2089500000E+00  -2.9338870000E-01   3.8796720000E-01
  9.1788000000E-01  -7.4156950000E-01   5.0902580000E-01
  3.6341200000E-01  -1.9094100000E-01   1.8038400000E-01
0 1 3 2.0 1.0   
  1.3927810000E+00   6.1397030000E-02  -1.8912650000E-01
  5.4391300000E-01   3.0611300000E-01   8.0054530000E-02
  9.1476000000E-02  -1.1548900000E+00   9.8773990000E-01
0 1 1 0.0 1.0   
  3.4312000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 3.0 1.0   
  1.6050250000E+01   8.5998990000E-02   
  4.1600630000E+00   3.8029960000E-01   
  1.2432650000E+00   7.1276590000E-01   
0 3 1 0.0 1.0   
  3.4427700000E-01   1.0000000000E+00   

24  7
0 0 6 2.0 1.00   
  5.1789810000E+04   1.7761820000E-03   
  7.7768490000E+03   1.3604760000E-02   
  1.7713850000E+03   6.7069250000E-02   
  4.9915880000E+02   2.3231040000E-01   
  1.5979820000E+02   4.8024100000E-01   
  5.4470210000E+01   3.4876530000E-01   
0 1 6 8.0 1.0   
  1.0643280000E+03   2.3996690000E-03   3.9869970000E-03
  2.5321380000E+02   3.1948860000E-02   3.1046620000E-02
  8.1609240000E+01   1.2508680000E-01   1.3505180000E-01
  3.0481930000E+01  -3.2218660000E-02   3.4488650000E-01
  1.2294390000E+01  -6.1722840000E-01   4.6285710000E-01
  5.0377220000E+00  -4.5259360000E-01   2.1104260000E-01
0 1 6 8.0 1.0   
  4.1562910000E+01  -3.4542160000E-03  -6.7224970000E-03
  1.3676270000E+01   7.2184280000E-02  -2.8064710000E-02
  5.8443900000E+00   2.5448200000E-01   5.8200280000E-02
  2.4716090000E+00  -2.9345340000E-01   3.9169880000E-01
  1.0283080000E+00  -7.3854550000E-01   5.0478230000E-01
  4.0725000000E-01  -1.9471570000E-01   1.7902900000E-01
0 1 3 2.0 1.0   
  1.5714640000E+00   5.8922190000E-02  -1.9301000000E-01
  6.0558000000E-01   2.9760550000E-01   9.6056200000E-02
  9.8561000000E-02  -1.1475060000E+00   9.8176090000E-01
0 1 1 0.0 1.0   
  3.6459000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 4.0 1.0   
  1.8419300000E+01   8.6508160000E-02   
  4.8126610000E+00   3.8266990000E-01   
  1.4464470000E+00   7.0937720000E-01   
0 3 1 0.0 1.0   
  4.0041300000E-01   1.0000000000E+00   

25  7
0 0 6 2.0 1.00   
  5.6347140000E+04   1.7715800000E-03   
  8.4609430000E+03   1.3570810000E-02   
  1.9273250000E+03   6.6906050000E-02   
  5.4323430000E+02   2.3185410000E-01   
  1.7399050000E+02   4.7990460000E-01   
  5.9360050000E+01   3.4957370000E-01   
0 1 6 8.0 1.0   
  1.1654120000E+03   2.3887510000E-03   3.9773180000E-03
  2.7732760000E+02   3.1817080000E-02   3.1031120000E-02
  8.9472780000E+01   1.2546700000E-01   1.3518940000E-01
  3.3482560000E+01  -2.9554310000E-02   3.4573870000E-01
  1.3540370000E+01  -6.1751600000E-01   4.6292050000E-01
  5.5579720000E+00  -4.5444580000E-01   2.0905920000E-01
0 1 6 8.0 1.0   
  4.5835320000E+01  -3.6658560000E-03  -6.8875780000E-03
  1.5187770000E+01   7.2319710000E-02  -2.8468160000E-02
  6.5007100000E+00   2.5444860000E-01   6.0318320000E-02
  2.7515830000E+00  -2.9103800000E-01   3.9389610000E-01
  1.1454040000E+00  -7.3598600000E-01   5.0137690000E-01
  4.5368700000E-01  -1.9976170000E-01   1.7922640000E-01
0 1 3 2.0 1.0   
  1.7579990000E+00   5.6285720000E-02  -5.0350240000E-01
  6.6702200000E-01   2.8974910000E-01   2.3450110000E-01
  1.0512900000E-01  -1.1406530000E+00   9.1412570000E-01
0 1 1 0.0 1.0   
  3.8418000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 5.0 1.0   
  2.0943550000E+01   8.6727020000E-02   
  5.5104860000E+00   3.8418830000E-01   
  1.6650380000E+00   7.0690710000E-01   
0 3 1 0.0 1.0   
  4.6173300000E-01   1.0000000000E+00   

26  7
0 0 6 2.0 1.00   
  6.1132620000E+04   1.7661110000E-03   
  9.1793420000E+03   1.3530380000E-02   
  2.0908570000E+03   6.6731280000E-02   
  5.8924790000E+02   2.3148230000E-01   
  1.8875430000E+02   4.7970580000E-01   
  6.4446290000E+01   3.5019760000E-01   
0 1 6 8.0 1.0   
  1.2599800000E+03   2.4380140000E-03   4.0280190000E-03
  2.9987610000E+02   3.2240480000E-02   3.1446470000E-02
  9.6849170000E+01   1.2657240000E-01   1.3683170000E-01
  3.6310200000E+01  -3.1399020000E-02   3.4872360000E-01
  1.4729960000E+01  -6.2075930000E-01   4.6179310000E-01
  6.0660750000E+00  -4.5029140000E-01   2.0430580000E-01
0 1 6 8.0 1.0   
  5.0434850000E+01  -3.8732560000E-03  -7.0171280000E-03
  1.6839290000E+01   7.1965980000E-02  -2.8776600000E-02
  7.1920860000E+00   2.5565910000E-01   6.1813830000E-02
  3.0534200000E+00  -2.8828370000E-01   3.9549460000E-01
  1.2736430000E+00  -7.3428220000E-01   4.9890590000E-01
  5.0409100000E-01  -2.0493530000E-01   1.7912510000E-01
0 1 3 2.0 1.0   
  1.9503160000E+00   5.6948690000E-02  -4.5937960000E-01
  7.3672100000E-01   2.8829150000E-01   2.8521390000E-01
  1.1417700000E-01  -1.1381590000E+00   9.0764850000E-01
0 1 1 0.0 1.0   
  4.1148000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 6.0 1.0   
  2.3149940000E+01   8.8769350000E-02   
  6.1223680000E+00   3.8963190000E-01   
  1.8466010000E+00   7.0148160000E-01   
0 3 1 0.0 1.0   
  5.0436100000E-01   1.0000000000E+00   

27  7
0 0 6 2.0 1.00   
  6.6148990000E+04   1.7597870000E-03   
  9.9330770000E+03   1.3481620000E-02   
  2.2628160000E+03   6.6493420000E-02   
  6.3791540000E+02   2.3079390000E-01   
  2.0441220000E+02   4.7929190000E-01   
  6.9825380000E+01   3.5140970000E-01   
0 1 6 8.0 1.0   
  1.3788410000E+03   2.3762760000E-03   3.9714880000E-03
  3.2826940000E+02   3.1674500000E-02   3.1081740000E-02
  1.0609460000E+02   1.2628880000E-01   1.3574390000E-01
  3.9832750000E+01  -2.5845520000E-02   3.4768270000E-01
  1.6186220000E+01  -6.1834910000E-01   4.6263400000E-01
  6.6677880000E+00  -4.5670080000E-01   2.0516320000E-01
0 1 6 8.0 1.0   
  5.4523550000E+01  -3.9930040000E-03  -7.2907720000E-03
  1.8297830000E+01   7.4096630000E-02  -2.9260270000E-02
  7.8673480000E+00   2.5420000000E-01   6.5641500000E-02
  3.3405340000E+00  -2.9216570000E-01   4.0006520000E-01
  1.3937560000E+00  -7.3187030000E-01   4.9502360000E-01
  5.5132600000E-01  -2.0407840000E-01   1.7582400000E-01
0 1 3 2.0 1.0   
  2.1519470000E+00   5.3798430000E-02  -2.1654960000E-01
  8.1106300000E-01   2.7599710000E-01   1.2404880000E-01
  1.2101700000E-01  -1.1296920000E+00   9.7240640000E-01
0 1 1 0.0 1.0   
  4.3037000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 7.0 1.0   
  2.5593060000E+01   9.0047480000E-02   
  6.8009900000E+00   3.9317030000E-01   
  2.0516470000E+00   6.9768440000E-01   
0 3 1 0.0 1.0   
  5.5567100000E-01   1.0000000000E+00   

28  7
0 0 6 2.0 1.00   
  7.1396350000E+04   1.7530030000E-03   
  1.0720840000E+04   1.3431220000E-02   
  2.4421290000E+03   6.6270410000E-02   
  6.8842650000E+02   2.3025080000E-01   
  2.2061530000E+02   4.7901860000E-01   
  7.5393730000E+01   3.5234440000E-01   
0 1 6 8.0 1.0   
  1.4925320000E+03   2.3707140000E-03   3.9675540000E-03
  3.5540130000E+02   3.1605660000E-02   3.1094790000E-02
  1.1495340000E+02   1.2663350000E-01   1.3595170000E-01
  4.3220430000E+01  -2.4170370000E-02   3.4851360000E-01
  1.7597100000E+01  -6.1877750000E-01   4.6254980000E-01
  7.2577650000E+00  -4.5767700000E-01   2.0351860000E-01
0 1 6 8.0 1.0   
  5.9352610000E+01  -4.1620020000E-03  -7.4214520000E-03
  2.0021810000E+01   7.4251110000E-02  -2.9534100000E-02
  8.6145610000E+00   2.5413600000E-01   6.7318520000E-02
  3.6605310000E+00  -2.9034770000E-01   4.0166600000E-01
  1.5281110000E+00  -7.3021210000E-01   4.9266230000E-01
  6.0405700000E-01  -2.0760570000E-01   1.7568930000E-01
0 1 3 2.0 1.0   
  2.3792760000E+00   5.1578880000E-02  -1.8876630000E-01
  8.8583900000E-01   2.7076110000E-01   1.0151990000E-01
  1.2852900000E-01  -1.1247700000E+00   9.7909060000E-01
0 1 1 0.0 1.0   
  4.5195000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 8.0 1.0   
  2.8191470000E+01   9.0988810000E-02   
  7.5235840000E+00   3.9582080000E-01   
  2.2712280000E+00   6.9471540000E-01   
0 3 1 0.0 1.0   
  6.1160300000E-01   1.0000000000E+00   

29  7
0 0 6 2.0 1.00   
  7.6794380000E+04   1.7481610000E-03   
  1.1530700000E+04   1.3396020000E-02   
  2.6265750000E+03   6.6108850000E-02   
  7.4049030000E+02   2.2982650000E-01   
  2.3735280000E+02   4.7876750000E-01   
  8.1158180000E+01   3.5307390000E-01   
0 1 6 8.0 1.0   
  1.6108140000E+03   2.3640550000E-03   3.9633070000E-03
  3.8363670000E+02   3.1536350000E-02   3.1102230000E-02
  1.2417330000E+02   1.2694520000E-01   1.3613500000E-01
  4.6746780000E+01  -2.2628400000E-02   3.4929140000E-01
  1.9065690000E+01  -6.1920800000E-01   4.6247800000E-01
  7.8715670000E+00  -4.5853930000E-01   2.0201020000E-01
0 1 6 8.0 1.0   
  6.4457320000E+01  -4.3310750000E-03  -7.5237250000E-03
  2.1852120000E+01   7.4123070000E-02  -2.9756870000E-02
  9.4053430000E+00   2.5421080000E-01   6.8496540000E-02
  3.9991680000E+00  -2.8748430000E-01   4.0271410000E-01
  1.6702970000E+00  -7.2914360000E-01   4.9084900000E-01
  6.5962700000E-01  -2.1139510000E-01   1.7592680000E-01
0 1 3 2.0 1.0   
  2.6000880000E+00   5.0275770000E-02  -1.7029110000E-01
  9.6309400000E-01   2.6500400000E-01   9.3101330000E-02
  1.3616100000E-01  -1.1201550000E+00   9.8143360000E-01
0 1 1 0.0 1.0   
  4.7332000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 9.0 1.0   
  3.0853410000E+01   9.1999050000E-02   
  8.2649850000E+00   3.9850210000E-01   
  2.4953320000E+00   6.9178970000E-01   
0 3 1 0.0 1.0   
  6.6765800000E-01   1.0000000000E+00   

30  7
0 0 6 2.0 1.00   
  8.2400940000E+04   1.7433290000E-03   
  1.2372550000E+04   1.3359660000E-02   
  2.8183510000E+03   6.5943650000E-02   
  7.9457170000E+02   2.2941510000E-01   
  2.5472320000E+02   4.7854530000E-01   
  8.7138800000E+01   3.5377530000E-01   
0 1 6 8.0 1.0   
  1.7325690000E+03   2.3614590000E-03   3.9631250000E-03
  4.1271490000E+02   3.1501770000E-02   3.1134110000E-02
  1.3367800000E+02   1.2727740000E-01   1.3639310000E-01
  5.0385850000E+01  -2.1459280000E-02   3.5012660000E-01
  2.0583580000E+01  -6.1976520000E-01   4.6231790000E-01
  8.5059400000E+00  -4.5901800000E-01   2.0049950000E-01
0 1 6 8.0 1.0   
  6.9364920000E+01  -4.4400980000E-03  -7.6892620000E-03
  2.3620820000E+01   7.5052530000E-02  -2.9979820000E-02
  1.0184710000E+01   2.5331110000E-01   7.0824110000E-02
  4.3340820000E+00  -2.8818970000E-01   4.0461410000E-01
  1.8109180000E+00  -7.2670520000E-01   4.8823250000E-01
  7.1484100000E-01  -2.1334390000E-01   1.7519700000E-01
0 1 3 2.0 1.0   
  2.8238420000E+00   4.8985430000E-02  -1.5867630000E-01
  1.0395430000E+00   2.5927930000E-01   8.3793270000E-02
  1.4326400000E-01  -1.1157110000E+00   9.8405470000E-01
0 1 1 0.0 1.0   
  4.9296000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 10.0 1.0   
  3.3707640000E+01   9.2626480000E-02   
  9.0611060000E+00   4.0029800000E-01   
  2.7383830000E+00   6.8966080000E-01   
0 3 1 0.0 1.0   
  7.3029400000E-01   1.0000000000E+00   


The 6-31G(d,p) Gaussian-Type Basis Sets

In order and in CRYSTAL format below:

1  3      
0 0 3 1.0 1.0
  1.8731136960E+01   3.3494604340E-02    
  2.8253943650E+00   2.3472695350E-01    
  6.4012169230E-01   8.1375732620E-01    
0 0 1 0.0 1.0
  1.6127775880E-01   1.0000000000E+00    
0 2 1 0.0 1.0
  1.1000000000E+00   1.0000000000E+00    

2  3    
0 0 3 2.0 1.0
  3.8421634000E+01   2.3766000000E-02
  5.7780300000E+00   1.5467900000E-01
  1.2417740000E+00   4.6963000000E-01
0 0 1 0.0 1.0
  2.9796400000E-01   1.0000000000E+00
0 2 1 0.0 1.0
  1.1000000000E+00   1.0000000000E+00
  
3  4      
0 0 6 2.0 1.0
  6.4241892000E+02   2.1426000000E-03
  9.6798515000E+01   1.6208900000E-02
  2.2091121000E+01   7.7315600000E-02
  6.2010703000E+00   2.4578600000E-01
  1.9351177000E+00   4.7018900000E-01
  6.3673580000E-01   3.4547080000E-01
0 1 3 1.0 1.0
  2.3249184000E+00  -3.5091700000E-02   8.9415000000E-03
  6.3243060000E-01  -1.9123280000E-01   1.4100950000E-01
  7.9053400000E-02   1.0839878000E+00   9.4536370000E-01
0 1 1 0.0 1.0
  3.5962000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 1 0.0 1.0
  2.0000000000E-01   1.0000000000E+00

4  4      
0 0 6 2.0 1.0
  1.2645857000E+03   1.9448000000E-03
  1.8993681000E+02   1.4835100000E-02
  4.3159089000E+01   7.2090600000E-02
  1.2098663000E+01   2.3715420000E-01
  3.8063232000E+00   4.6919870000E-01
  1.2728903000E+00   3.5652020000E-01
0 1 3 2.0 1.0
  3.1964631000E+00  -1.1264870000E-01   5.5980200000E-02
  7.4781330000E-01  -2.2950640000E-01   2.6155060000E-01
  2.1996630000E-01   1.1869167000E+00   7.9397230000E-01
0 1 1 0.0 1.0
  8.2309900000E-02   1.0000000000E+00   1.0000000000E+00
0 3 1 0.0 1.0
  4.0000000000E-01   1.0000000000E+00

5  4      
0 0 6 2.0 1.0
  2.0688823000E+03   1.8663000000E-03
  3.1064957000E+02   1.4251500000E-02
  7.0683033000E+01   6.9551600000E-02
  1.9861080000E+01   2.3257290000E-01
  6.2993048000E+00   4.6707870000E-01
  2.1270270000E+00   3.6343140000E-01
0 1 3 3.0 1.0
  4.7279710000E+00  -1.3039380000E-01   7.4597600000E-02
  1.1903377000E+00  -1.3078890000E-01   3.0784670000E-01
  3.5941170000E-01   1.1309444000E+00   7.4345680000E-01
0 1 1 0.0 1.0
  1.2675120000E-01   1.0000000000E+00   1.0000000000E+00
0 3 1 0.0 1.0
  6.0000000000E-01   1.0000000000E+00

6  4      
0 0 6 2.0 1.0
  3.0475248800E+03   1.8347371300E-03    
  4.5736951800E+02   1.4037322800E-02    
  1.0394868500E+02   6.8842622200E-02    
  2.9210155300E+01   2.3218444300E-01    
  9.2866629600E+00   4.6794134800E-01    
  3.1639269600E+00   3.6231198500E-01    
0 1 3 4.0 1.0
  7.8682723500E+00  -1.1933242000E-01   6.8999066600E-02  
  1.8812885400E+00  -1.6085415200E-01   3.1642396100E-01  
  5.4424925800E-01   1.1434564400E+00   7.4430829100E-01  
0 1 1 0.0 1.0
  1.6871447820E-01   1.0000000000E+00   1.0000000000E+00  
0 3 1 0.0 1.0
  8.0000000000E-01   1.0000000000E+00    

7  4      
0 0 6 2.0 1.0
  4.1735110000E+03   1.8348000000E-03    
  6.2745790000E+02   1.3995000000E-02    
  1.4290210000E+02   6.8587000000E-02    
  4.0234330000E+01   2.3224100000E-01    
  1.2820210000E+01   4.6907000000E-01    
  4.3904370000E+00   3.6045500000E-01    
0 1 3 5.0 1.0
  1.1626358000E+01  -1.1496100000E-01   6.7580000000E-02  
  2.7162800000E+00  -1.6911800000E-01   3.2390700000E-01  
  7.7221800000E-01   1.1458520000E+00   7.4089500000E-01  
0 1 1 0.0 1.0
  2.1203130000E-01   1.0000000000E+00   1.0000000000E+00  
0 3 1 0.0 1.0
  8.0000000000E-01   1.0000000000E+00    

8  4      
0 0 6 2.0 1.0
  5.4846717000E+03   1.8311000000E-03    
  8.2523495000E+02   1.3950100000E-02    
  1.8804696000E+02   6.8445100000E-02    
  5.2964500000E+01   2.3271430000E-01    
  1.6897570000E+01   4.7019300000E-01    
  5.7996353000E+00   3.5852090000E-01    
0 1 3 6.0 1.0
  1.5539616000E+01  -1.1077750000E-01   7.0874300000E-02  
  3.5999336000E+00  -1.4802630000E-01   3.3975280000E-01  
  1.0137618000E+00   1.1307670000E+00   7.2715860000E-01  
0 1 1 0.0 1.0
  2.7000580000E-01   1.0000000000E+00   1.0000000000E+00  
0 3 1 0.0 1.0
  8.0000000000E-01   1.0000000000E+00    

9  4      
0 0 6 2.0 1.0
  7.0017130900E+03   1.8196169000E-03
  1.0513660900E+03   1.3916079600E-02
  2.3928569000E+02   6.8405324500E-02
  6.7397445300E+01   2.3318576000E-01
  2.1519957300E+01   4.7126743900E-01
  7.4031013000E+00   3.5661854600E-01
0 1 3 7.0 1.0
  2.0847952800E+01  -1.0850697500E-01   7.1628724300E-02
  4.8083083400E+00  -1.4645165800E-01   3.4591210300E-01
  1.3440698600E+00   1.1286885800E+00   7.2246995700E-01
0 1 1 0.0 1.0
  3.5815139300E-01   1.0000000000E+00   1.0000000000E+00
0 3 1 0.0 1.0
  8.0000000000E-01   1.0000000000E+00

10  4    
0 0 6 2.0 1.0
  8.4258515300E+03   1.8843481000E-03
  1.2685194000E+03   1.4336899400E-02
  2.8962141400E+02   7.0109623300E-02
  8.1859004000E+01   2.3737326600E-01
  2.6251507900E+01   4.7300712600E-01
  9.0947205100E+00   3.4840124100E-01
0 1 3 8.0 1.0
  2.6532131000E+01  -1.0711828700E-01   7.1909588500E-02
  6.1017550100E+00  -1.4616382100E-01   3.4951337200E-01
  1.6962715300E+00   1.1277735000E+00   7.1994051200E-01
0 1 1 0.0 1.0
  4.4581870000E-01   1.0000000000E+00   1.0000000000E+00
0 3 1 0.0 1.0
  8.0000000000E-01   1.0000000000E+00

11  5
0 0 6 2.0 1.0
  9.9932000000E+03   1.9377000000E-03
  1.4998900000E+03   1.4807000000E-02
  3.4195100000E+02   7.2706000000E-02
  9.4679700000E+01   2.5262900000E-01
  2.9734500000E+01   4.9324200000E-01
  1.0006300000E+01   3.1316900000E-01
0 1 6 8.0 1.0
  1.5096300000E+02  -3.5421000000E-03   5.0017000000E-03      
  3.5587800000E+01  -4.3959000000E-02   3.5511000000E-02      
  1.1168300000E+01  -1.0975210000E-01   1.4282500000E-01      
  3.9020100000E+00   1.8739800000E-01   3.3862000000E-01      
  1.3817700000E+00   6.4669900000E-01   4.5157900000E-01      
  4.6638200000E-01   3.0605800000E-01   2.7327100000E-01      
0 1 3 1.0 1.0
  4.9796600000E-01  -2.4850300000E-01  -2.3023000000E-02      
  8.4353000000E-02  -1.3170400000E-01   9.5035900000E-01      
  6.6635000000E-02   1.2335200000E+00   5.9858000000E-02      
0 1 1 0.0 1.0
  2.5954400000E-02   1.0000000000E+00   1.0000000000E+00      
0 3 1 0.0 1.0
  1.7500000000E-01   1.0000000000E+00         

12  5 
0 0 6 2.0 1.0
  1.1722800000E+04   1.9778000000E-03         
  1.7599300000E+03   1.5114000000E-02         
  4.0084600000E+02   7.3911000000E-02         
  1.1280700000E+02   2.4919100000E-01         
  3.5999700000E+01   4.8792800000E-01         
  1.2182800000E+01   3.1966200000E-01         
0 1 6 8.0 1.0
  1.8918000000E+02  -3.2372000000E-03   4.9281000000E-03      
  4.5211900000E+01  -4.1008000000E-02   3.4989000000E-02      
  1.4356300000E+01  -1.1260000000E-01   1.4072500000E-01      
  5.1388600000E+00   1.4863300000E-01   3.3364200000E-01      
  1.9065200000E+00   6.1649700000E-01   4.4494000000E-01      
  7.0588700000E-01   3.6482900000E-01   2.6925400000E-01      
0 1 3 2.0 1.0
  9.2934000000E-01  -2.1229000000E-01  -2.2419000000E-02      
  2.6903500000E-01  -1.0798500000E-01   1.9227000000E-01      
  1.1737900000E-01   1.1758400000E+00   8.4618100000E-01      
0 1 1 0.0 1.0
  4.2106100000E-02   1.0000000000E+00   1.0000000000E+00      
0 3 1 0.0 1.0
  1.7500000000E-01   1.0000000000E+00         
  
13  5
0 0 6 2.0 1.0
  1.3983100000E+04   1.9426700000E-03         
  2.0987500000E+03   1.4859900000E-02         
  4.7770500000E+02   7.2849400000E-02         
  1.3436000000E+02   2.4683000000E-01         
  4.2870900000E+01   4.8725800000E-01         
  1.4518900000E+01   3.2349600000E-01         
0 1 6 8.0 1.0
  2.3966800000E+02  -2.9261900000E-03   4.6028500000E-03      
  5.7441900000E+01  -3.7408000000E-02   3.3199000000E-02      
  1.8285900000E+01  -1.1448700000E-01   1.3628200000E-01      
  6.5991400000E+00   1.1563500000E-01   3.3047600000E-01      
  2.4904900000E+00   6.1259500000E-01   4.4914600000E-01      
  9.4454000000E-01   3.9379900000E-01   2.6570400000E-01      
0 1 3 3.0 1.0
  1.2779000000E+00  -2.2760600000E-01  -1.7513000000E-02      
  3.9759000000E-01   1.4458300000E-03   2.4453300000E-01      
  1.6009500000E-01   1.0927900000E+00   8.0493400000E-01      
0 1 1 0.0 1.0
  5.5657700000E-02   1.0000000000E+00   1.0000000000E+00      
0 3 1 0.0 1.0
  3.2500000000E-01   1.0000000000E+00         
  
14  5
0 0 6 2.0 1.0
  1.6115900000E+04   1.9594800000E-03         
  2.4255800000E+03   1.4928800000E-02         
  5.5386700000E+02   7.2847800000E-02         
  1.5634000000E+02   2.4613000000E-01         
  5.0068300000E+01   4.8591400000E-01         
  1.7017800000E+01   3.2500200000E-01         
0 1 6 8.0 1.0
  2.9271800000E+02  -2.7809400000E-03   4.4382600000E-03      
  6.9873100000E+01  -3.5714600000E-02   3.2667900000E-02      
  2.2336300000E+01  -1.1498500000E-01   1.3472100000E-01      
  8.1503900000E+00   9.3563400000E-02   3.2867800000E-01      
  3.1345800000E+00   6.0301700000E-01   4.4964000000E-01      
  1.2254300000E+00   4.1895900000E-01   2.6137200000E-01      
0 1 3 4.0 1.0
  1.7273800000E+00  -2.4463000000E-01  -1.7795100000E-02      
  5.7292200000E-01   4.3157200000E-03   2.5353900000E-01      
  2.2219200000E-01   1.0981800000E+00   8.0066900000E-01      
0 1 1 0.0 1.0
  7.7836900000E-02   1.0000000000E+00   1.0000000000E+00      
0 3 1 0.0 1.0
  4.5000000000E-01   1.0000000000E+00         

15  5
0 0 6 2.0 1.0
  1.9413300000E+04   1.8516000000E-03         
  2.9094200000E+03   1.4206200000E-02         
  6.6136400000E+02   6.9999500000E-02         
  1.8575900000E+02   2.4007900000E-01         
  5.9194300000E+01   4.8476200000E-01         
  2.0031000000E+01   3.3520000000E-01         
0 1 6 8.0 1.0
  3.3947800000E+02  -2.7821700000E-03   4.5646200000E-03      
  8.1010100000E+01  -3.6049900000E-02   3.3693600000E-02      
  2.5878000000E+01  -1.1663100000E-01   1.3975500000E-01      
  9.4522100000E+00   9.6832800000E-02   3.3936200000E-01      
  3.6656600000E+00   6.1441800000E-01   4.5092100000E-01      
  1.4674600000E+00   4.0379800000E-01   2.3858600000E-01      
0 1 3 5.0 1.0
  2.1562300000E+00  -2.5292300000E-01  -1.7765300000E-02      
  7.4899700000E-01   3.2851700000E-02   2.7405800000E-01      
  2.8314500000E-01   1.0812500000E+00   7.8542100000E-01      
0 1 1 0.0 1.0
  9.9831700000E-02   1.0000000000E+00   1.0000000000E+00      
0 3 1 0.0 1.0
  5.5000000000E-01   1.0000000000E+00         
  
16  5
0 0 6 2.0 1.0
  2.1917100000E+04   1.8690000000E-03         
  3.3014900000E+03   1.4230000000E-02         
  7.5414600000E+02   6.9696000000E-02         
  2.1271100000E+02   2.3848700000E-01         
  6.7989600000E+01   4.8330700000E-01         
  2.3051500000E+01   3.3807400000E-01         
0 1 6 8.0 1.0
  4.2373500000E+02  -2.3767000000E-03   4.0610000000E-03      
  1.0071000000E+02  -3.1693000000E-02   3.0681000000E-02      
  3.2159900000E+01  -1.1331700000E-01   1.3045200000E-01      
  1.1807900000E+01   5.6090000000E-02   3.2720500000E-01      
  4.6311000000E+00   5.9225500000E-01   4.5285100000E-01      
  1.8702500000E+00   4.5500600000E-01   2.5604200000E-01      
0 1 3 6.0 1.0
  2.6158400000E+00  -2.5037400000E-01  -1.4511000000E-02      
  9.2216700000E-01   6.6957000000E-02   3.1026300000E-01      
  3.4128700000E-01   1.0545100000E+00   7.5448300000E-01      
0 1 1 0.0 1.0
  1.1716700000E-01   1.0000000000E+00   1.0000000000E+00      
0 3 1 0.0 1.0
  6.5000000000E-01   1.0000000000E+00         

17  5
0 0 6 2.0 1.0
  2.5180100000E+04   1.8330000000E-03         
  3.7803500000E+03   1.4034000000E-02         
  8.6047400000E+02   6.9097000000E-02         
  2.4214500000E+02   2.3745200000E-01         
  7.7334900000E+01   4.8303400000E-01         
  2.6247000000E+01   3.3985600000E-01         
0 1 6 8.0 1.0
  4.9176500000E+02  -2.2974000000E-03   3.9894000000E-03      
  1.1698400000E+02  -3.0714000000E-02   3.0318000000E-02      
  3.7415300000E+01  -1.1252800000E-01   1.2988000000E-01      
  1.3783400000E+01   4.5016000000E-02   3.2795100000E-01      
  5.4521500000E+00   5.8935300000E-01   4.5352700000E-01      
  2.2258800000E+00   4.6520600000E-01   2.5215400000E-01      
0 1 3 7.0 1.0
  3.1864900000E+00  -2.5183000000E-01  -1.4299000000E-02      
  1.1442700000E+00   6.1589000000E-02   3.2357200000E-01      
  4.2037700000E-01   1.0601800000E+00   7.4350700000E-01      
0 1 1 0.0 1.0
  1.4265700000E-01   1.0000000000E+00   1.0000000000E+00      
0 3 1 0.0 1.0
  7.5000000000E-01   1.0000000000E+00         
  
18  5
0 0 6 2.0 1.0
  2.8348300000E+04   1.8252600000E-03         
  4.2576200000E+03   1.3968600000E-02         
  9.6985700000E+02   6.8707300000E-02         
  2.7326300000E+02   2.3620400000E-01         
  8.7369500000E+01   4.8221400000E-01         
  2.9686700000E+01   3.4204300000E-01         
0 1 6 8.0 1.0
  5.7589100000E+02  -2.1597200000E-03   3.8066500000E-03      
  1.3681600000E+02  -2.9077500000E-02   2.9230500000E-02      
  4.3809800000E+01  -1.1082700000E-01   1.2646700000E-01      
  1.6209400000E+01   2.7699900000E-02   3.2351000000E-01      
  6.4608400000E+00   5.7761300000E-01   4.5489600000E-01      
  2.6511400000E+00   4.8868800000E-01   2.5663000000E-01      
0 1 3 8.0 1.0
  3.8602800000E+00  -2.5559200000E-01  -1.5919700000E-02      
  1.4137300000E+00   3.7806600000E-02   3.2464600000E-01      
  5.1664600000E-01   1.0805600000E+00   7.4399000000E-01      
0 1 1 0.0 1.0
  1.7388800000E-01   1.0000000000E+00   1.0000000000E+00      
0 3 1 0.0 1.0
  8.5000000000E-01   1.0000000000E+00         

19  6
0 0 6 2.0 1.0
  3.1594420000E+04   1.8280100000E-03         
  4.7443300000E+03   1.3994030000E-02         
  1.0804190000E+03   6.8871290000E-02         
  3.0423380000E+02   2.3697600000E-01         
  9.7245860000E+01   4.8290400000E-01         
  3.3024950000E+01   3.4047950000E-01         
0 1 6 8.0 1.0
  6.2276250000E+02  -2.5029760000E-03   4.0946370000E-03      
  1.4788390000E+02  -3.3155500000E-02   3.1451990000E-02      
  4.7327350000E+01  -1.2263870000E-01   1.3515580000E-01      
  1.7514950000E+01   5.3536430000E-02   3.3905000000E-01      
  6.9227220000E+00   6.1938600000E-01   4.6294550000E-01      
  2.7682770000E+00   4.3458780000E-01   2.2426380000E-01      
0 1 6 8.0 1.0
  1.1848020000E+01   1.2776890000E-02  -1.2213770000E-02      
  4.0792110000E+00   2.0987670000E-01  -6.9005370000E-03      
  1.7634810000E+00  -3.0952740000E-03   2.0074660000E-01      
  7.8892700000E-01  -5.5938840000E-01   4.2813320000E-01      
  3.5038700000E-01  -5.1347600000E-01   3.9701560000E-01      
  1.4634400000E-01  -6.5980350000E-02   1.1047180000E-01      
0 1 3 1.0 1.0
  7.1680100000E-01  -5.2377720000E-02   3.1643000000E-02      
  2.3374100000E-01  -2.7985030000E-01  -4.0461600000E-02      
  3.8675000000E-02   1.1415470000E+00   1.0120290000E+00      
0 1 1 0.0 1.0
  1.6521000000E-02   1.0000000000E+00   1.0000000000E+00      
0 3 1 0.0 1.0
  2.0000000000E-01   1.0000000000E+00         
  
20  6
0 0 6 2.0 1.0
  3.5264860000E+04   1.8135010000E-03         
  5.2955030000E+03   1.3884930000E-02         
  1.2060200000E+03   6.8361620000E-02         
  3.3968390000E+02   2.3561880000E-01         
  1.0862640000E+02   4.8206390000E-01         
  3.6921030000E+01   3.4298190000E-01         
0 1 6 8.0 1.0
  7.0630960000E+02   2.4482250000E-03   4.0203710000E-03      
  1.6781870000E+02   3.2415040000E-02   3.1006010000E-02      
  5.3825580000E+01   1.2262190000E-01   1.3372790000E-01      
  2.0016380000E+01  -4.3169650000E-02   3.3679830000E-01      
  7.9702790000E+00  -6.1269950000E-01   4.6312810000E-01      
  3.2120590000E+00  -4.4875400000E-01   2.2575320000E-01      
0 1 6 8.0 1.0
  1.4195180000E+01   1.0845000000E-02  -1.2896210000E-02      
  4.8808280000E+00   2.0883330000E-01  -1.0251980000E-02      
  2.1603900000E+00   3.1503380000E-02   1.9597810000E-01      
  9.8789900000E-01  -5.5265180000E-01   4.3579330000E-01      
  4.4951700000E-01  -5.4379970000E-01   3.9964520000E-01      
  1.8738700000E-01  -6.6693420000E-02   9.7136360000E-02      
0 1 3 1.0 1.0
  1.0322710000E+00  -4.4397200000E-02  -4.2986210000E-01      
  3.8117100000E-01  -3.2845630000E-01   6.9358290000E-03      
  6.5131000000E-02   1.1630100000E+00   9.7059330000E-01      
0 1 1 0.0 1.0
  2.6010000000E-02   1.0000000000E+00   1.0000000000E+00      
0 3 1 0.0 1.0
  2.0000000000E-01   1.0000000000E+00         

21  8
0 0 6 2.0 1.00
  3.9088980000E+04   1.8032630000E-03   
  5.8697920000E+03   1.3807690000E-02   
  1.3369100000E+03   6.8003960000E-02   
  3.7660310000E+02   2.3470990000E-01   
  1.2046790000E+02   4.8156900000E-01   
  4.0980320000E+01   3.4456520000E-01   
0 1 6 8.0 1.0
  7.8628520000E+02   2.4518630000E-03   4.0395300000E-03
  1.8688700000E+02   3.2595790000E-02   3.1225700000E-02
  6.0009350000E+01   1.2382420000E-01   1.3498330000E-01
  2.2258830000E+01  -4.3598900000E-02   3.4247930000E-01
  8.8851490000E+00  -6.1771810000E-01   4.6231130000E-01
  3.6092110000E+00  -4.4328230000E-01   2.1775240000E-01
0 1 6 8.0 1.0
  2.9843550000E+01  -2.5863020000E-03  -6.0966520000E-03
  9.5423830000E+00   7.1884240000E-02  -2.6288840000E-02
  4.0567900000E+00   2.5032600000E-01   5.0910010000E-02
  1.7047030000E+00  -2.9910030000E-01   3.7980970000E-01
  7.0623400000E-01  -7.4468180000E-01   5.1708830000E-01
  2.7953600000E-01  -1.7997760000E-01   1.8297720000E-01
0 1 3 2.0 1.0
  1.0656090000E+00   6.4829780000E-02  -2.9384400000E-01
  4.2593300000E-01   3.2537560000E-01   9.2353230000E-02
  7.6320000000E-02  -1.1708060000E+00   9.8479300000E-01
0 1 1 0.0 1.0
  2.9594000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 1.0 1.0
  1.1147010000E+01   8.7476720000E-02   
  2.8210430000E+00   3.7956350000E-01   
  8.1962000000E-01   7.1803930000E-01   
0 3 1 0.0 1.0
  2.2146800000E-01   1.0000000000E+00   
0 4 1 0.0 1.0
  8.0000000000E-01   1.0000000000E+00   

22  8  
0 0 6 2.0 1.00
  4.3152950000E+04   1.7918720000E-03   
  6.4795710000E+03   1.3723920000E-02   
  1.4756750000E+03   6.7628300000E-02   
  4.1569910000E+02   2.3376420000E-01   
  1.3300060000E+02   4.8106960000E-01   
  4.5272220000E+01   3.4622800000E-01   
0 1 6 8.0 1.0   
  8.7468260000E+02   2.4310080000E-03   4.0176790000E-03
  2.0797850000E+02   3.2330270000E-02   3.1139660000E-02
  6.6879180000E+01   1.2425200000E-01   1.3490770000E-01
  2.4873470000E+01  -3.9039050000E-02   3.4316720000E-01
  9.9684410000E+00  -6.1717890000E-01   4.6257600000E-01
  4.0638260000E+00  -4.4730970000E-01   2.1546030000E-01
0 1 6 8.0 1.0   
  3.3643630000E+01  -2.9403580000E-03  -6.3116200000E-03
  1.0875650000E+01   7.1631030000E-02  -2.6976380000E-02
  4.6282250000E+00   2.5289150000E-01   5.3168470000E-02
  1.9501260000E+00  -2.9664010000E-01   3.8455490000E-01
  8.0945200000E-01  -7.4322150000E-01   5.1276620000E-01
  3.2047400000E-01  -1.8535200000E-01   1.8111350000E-01
0 1 3 2.0 1.0   
  1.2241480000E+00   6.3514650000E-02  -2.1120700000E-01
  4.8426300000E-01   3.1514040000E-01   7.7719980000E-02
  8.4096000000E-02  -1.1625950000E+00   9.8982140000E-01
0 1 1 0.0 1.0   
  3.2036000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 2.0 1.0   
  1.3690850000E+01   8.5894180000E-02   
  3.5131540000E+00   3.7846710000E-01   
  1.0404340000E+00   7.1612390000E-01   
0 3 1 0.0 1.0   
  2.8696200000E-01   1.0000000000E+00   
0 4 1 0.0 1.0   
  8.0000000000E-01   1.0000000000E+00   

23  8
0 0 6 2.0 1.00   
  4.7354330000E+04   1.7845130000E-03   
  7.1107870000E+03   1.3667540000E-02   
  1.6195910000E+03   6.7361220000E-02   
  4.5633790000E+02   2.3305520000E-01   
  1.4606060000E+02   4.8063160000E-01   
  4.9757910000E+01   3.4748020000E-01   
0 1 6 8.0 1.0   
  9.6814840000E+02   2.4105990000E-03   3.9950050000E-03
  2.3028210000E+02   3.2072430000E-02   3.1040610000E-02
  7.4145910000E+01   1.2459420000E-01   1.3477470000E-01
  2.7641070000E+01  -3.4821770000E-02   3.4372790000E-01
  1.1114750000E+01  -6.1673740000E-01   4.6287590000E-01
  4.5431130000E+00  -4.5098440000E-01   2.1355470000E-01
0 1 6 8.0 1.0   
  3.7640500000E+01  -3.2331990000E-03  -6.4940560000E-03
  1.2282380000E+01   7.1307440000E-02  -2.7534530000E-02
  5.2333660000E+00   2.5438200000E-01   5.5162840000E-02
  2.2089500000E+00  -2.9338870000E-01   3.8796720000E-01
  9.1788000000E-01  -7.4156950000E-01   5.0902580000E-01
  3.6341200000E-01  -1.9094100000E-01   1.8038400000E-01
0 1 3 2.0 1.0   
  1.3927810000E+00   6.1397030000E-02  -1.8912650000E-01
  5.4391300000E-01   3.0611300000E-01   8.0054530000E-02
  9.1476000000E-02  -1.1548900000E+00   9.8773990000E-01
0 1 1 0.0 1.0   
  3.4312000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 3.0 1.0   
  1.6050250000E+01   8.5998990000E-02   
  4.1600630000E+00   3.8029960000E-01   
  1.2432650000E+00   7.1276590000E-01   
0 3 1 0.0 1.0   
  3.4427700000E-01   1.0000000000E+00   
0 4 1 0.0 1.0   
  8.0000000000E-01   1.0000000000E+00   

24  8
0 0 6 2.0 1.00   
  5.1789810000E+04   1.7761820000E-03   
  7.7768490000E+03   1.3604760000E-02   
  1.7713850000E+03   6.7069250000E-02   
  4.9915880000E+02   2.3231040000E-01   
  1.5979820000E+02   4.8024100000E-01   
  5.4470210000E+01   3.4876530000E-01   
0 1 6 8.0 1.0   
  1.0643280000E+03   2.3996690000E-03   3.9869970000E-03
  2.5321380000E+02   3.1948860000E-02   3.1046620000E-02
  8.1609240000E+01   1.2508680000E-01   1.3505180000E-01
  3.0481930000E+01  -3.2218660000E-02   3.4488650000E-01
  1.2294390000E+01  -6.1722840000E-01   4.6285710000E-01
  5.0377220000E+00  -4.5259360000E-01   2.1104260000E-01
0 1 6 8.0 1.0   
  4.1562910000E+01  -3.4542160000E-03  -6.7224970000E-03
  1.3676270000E+01   7.2184280000E-02  -2.8064710000E-02
  5.8443900000E+00   2.5448200000E-01   5.8200280000E-02
  2.4716090000E+00  -2.9345340000E-01   3.9169880000E-01
  1.0283080000E+00  -7.3854550000E-01   5.0478230000E-01
  4.0725000000E-01  -1.9471570000E-01   1.7902900000E-01
0 1 3 2.0 1.0   
  1.5714640000E+00   5.8922190000E-02  -1.9301000000E-01
  6.0558000000E-01   2.9760550000E-01   9.6056200000E-02
  9.8561000000E-02  -1.1475060000E+00   9.8176090000E-01
0 1 1 0.0 1.0   
  3.6459000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 4.0 1.0   
  1.8419300000E+01   8.6508160000E-02   
  4.8126610000E+00   3.8266990000E-01   
  1.4464470000E+00   7.0937720000E-01   
0 3 1 0.0 1.0   
  4.0041300000E-01   1.0000000000E+00   
0 4 1 0.0 1.0   
  8.0000000000E-01   1.0000000000E+00   

25  8
0 0 6 2.0 1.00   
  5.6347140000E+04   1.7715800000E-03   
  8.4609430000E+03   1.3570810000E-02   
  1.9273250000E+03   6.6906050000E-02   
  5.4323430000E+02   2.3185410000E-01   
  1.7399050000E+02   4.7990460000E-01   
  5.9360050000E+01   3.4957370000E-01   
0 1 6 8.0 1.0   
  1.1654120000E+03   2.3887510000E-03   3.9773180000E-03
  2.7732760000E+02   3.1817080000E-02   3.1031120000E-02
  8.9472780000E+01   1.2546700000E-01   1.3518940000E-01
  3.3482560000E+01  -2.9554310000E-02   3.4573870000E-01
  1.3540370000E+01  -6.1751600000E-01   4.6292050000E-01
  5.5579720000E+00  -4.5444580000E-01   2.0905920000E-01
0 1 6 8.0 1.0   
  4.5835320000E+01  -3.6658560000E-03  -6.8875780000E-03
  1.5187770000E+01   7.2319710000E-02  -2.8468160000E-02
  6.5007100000E+00   2.5444860000E-01   6.0318320000E-02
  2.7515830000E+00  -2.9103800000E-01   3.9389610000E-01
  1.1454040000E+00  -7.3598600000E-01   5.0137690000E-01
  4.5368700000E-01  -1.9976170000E-01   1.7922640000E-01
0 1 3 2.0 1.0   
  1.7579990000E+00   5.6285720000E-02  -5.0350240000E-01
  6.6702200000E-01   2.8974910000E-01   2.3450110000E-01
  1.0512900000E-01  -1.1406530000E+00   9.1412570000E-01
0 1 1 0.0 1.0   
  3.8418000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 5.0 1.0   
  2.0943550000E+01   8.6727020000E-02   
  5.5104860000E+00   3.8418830000E-01   
  1.6650380000E+00   7.0690710000E-01   
0 3 1 0.0 1.0   
  4.6173300000E-01   1.0000000000E+00   
0 4 1 0.0 1.0   
  8.0000000000E-01   1.0000000000E+00   

26  8
0 0 6 2.0 1.00   
  6.1132620000E+04   1.7661110000E-03   
  9.1793420000E+03   1.3530380000E-02   
  2.0908570000E+03   6.6731280000E-02   
  5.8924790000E+02   2.3148230000E-01   
  1.8875430000E+02   4.7970580000E-01   
  6.4446290000E+01   3.5019760000E-01   
0 1 6 8.0 1.0   
  1.2599800000E+03   2.4380140000E-03   4.0280190000E-03
  2.9987610000E+02   3.2240480000E-02   3.1446470000E-02
  9.6849170000E+01   1.2657240000E-01   1.3683170000E-01
  3.6310200000E+01  -3.1399020000E-02   3.4872360000E-01
  1.4729960000E+01  -6.2075930000E-01   4.6179310000E-01
  6.0660750000E+00  -4.5029140000E-01   2.0430580000E-01
0 1 6 8.0 1.0   
  5.0434850000E+01  -3.8732560000E-03  -7.0171280000E-03
  1.6839290000E+01   7.1965980000E-02  -2.8776600000E-02
  7.1920860000E+00   2.5565910000E-01   6.1813830000E-02
  3.0534200000E+00  -2.8828370000E-01   3.9549460000E-01
  1.2736430000E+00  -7.3428220000E-01   4.9890590000E-01
  5.0409100000E-01  -2.0493530000E-01   1.7912510000E-01
0 1 3 2.0 1.0   
  1.9503160000E+00   5.6948690000E-02  -4.5937960000E-01
  7.3672100000E-01   2.8829150000E-01   2.8521390000E-01
  1.1417700000E-01  -1.1381590000E+00   9.0764850000E-01
0 1 1 0.0 1.0   
  4.1148000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 6.0 1.0   
  2.3149940000E+01   8.8769350000E-02   
  6.1223680000E+00   3.8963190000E-01   
  1.8466010000E+00   7.0148160000E-01   
0 3 1 0.0 1.0   
  5.0436100000E-01   1.0000000000E+00   
0 4 1 0.0 1.0   
  8.0000000000E-01   1.0000000000E+00   

27  8
0 0 6 2.0 1.00   
  6.6148990000E+04   1.7597870000E-03   
  9.9330770000E+03   1.3481620000E-02   
  2.2628160000E+03   6.6493420000E-02   
  6.3791540000E+02   2.3079390000E-01   
  2.0441220000E+02   4.7929190000E-01   
  6.9825380000E+01   3.5140970000E-01   
0 1 6 8.0 1.0   
  1.3788410000E+03   2.3762760000E-03   3.9714880000E-03
  3.2826940000E+02   3.1674500000E-02   3.1081740000E-02
  1.0609460000E+02   1.2628880000E-01   1.3574390000E-01
  3.9832750000E+01  -2.5845520000E-02   3.4768270000E-01
  1.6186220000E+01  -6.1834910000E-01   4.6263400000E-01
  6.6677880000E+00  -4.5670080000E-01   2.0516320000E-01
0 1 6 8.0 1.0   
  5.4523550000E+01  -3.9930040000E-03  -7.2907720000E-03
  1.8297830000E+01   7.4096630000E-02  -2.9260270000E-02
  7.8673480000E+00   2.5420000000E-01   6.5641500000E-02
  3.3405340000E+00  -2.9216570000E-01   4.0006520000E-01
  1.3937560000E+00  -7.3187030000E-01   4.9502360000E-01
  5.5132600000E-01  -2.0407840000E-01   1.7582400000E-01
0 1 3 2.0 1.0   
  2.1519470000E+00   5.3798430000E-02  -2.1654960000E-01
  8.1106300000E-01   2.7599710000E-01   1.2404880000E-01
  1.2101700000E-01  -1.1296920000E+00   9.7240640000E-01
0 1 1 0.0 1.0   
  4.3037000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 7.0 1.0   
  2.5593060000E+01   9.0047480000E-02   
  6.8009900000E+00   3.9317030000E-01   
  2.0516470000E+00   6.9768440000E-01   
0 3 1 0.0 1.0   
  5.5567100000E-01   1.0000000000E+00   
0 4 1 0.0 1.0   
  8.0000000000E-01   1.0000000000E+00   

28  8
0 0 6 2.0 1.00   
  7.1396350000E+04   1.7530030000E-03   
  1.0720840000E+04   1.3431220000E-02   
  2.4421290000E+03   6.6270410000E-02   
  6.8842650000E+02   2.3025080000E-01   
  2.2061530000E+02   4.7901860000E-01   
  7.5393730000E+01   3.5234440000E-01   
0 1 6 8.0 1.0   
  1.4925320000E+03   2.3707140000E-03   3.9675540000E-03
  3.5540130000E+02   3.1605660000E-02   3.1094790000E-02
  1.1495340000E+02   1.2663350000E-01   1.3595170000E-01
  4.3220430000E+01  -2.4170370000E-02   3.4851360000E-01
  1.7597100000E+01  -6.1877750000E-01   4.6254980000E-01
  7.2577650000E+00  -4.5767700000E-01   2.0351860000E-01
0 1 6 8.0 1.0   
  5.9352610000E+01  -4.1620020000E-03  -7.4214520000E-03
  2.0021810000E+01   7.4251110000E-02  -2.9534100000E-02
  8.6145610000E+00   2.5413600000E-01   6.7318520000E-02
  3.6605310000E+00  -2.9034770000E-01   4.0166600000E-01
  1.5281110000E+00  -7.3021210000E-01   4.9266230000E-01
  6.0405700000E-01  -2.0760570000E-01   1.7568930000E-01
0 1 3 2.0 1.0   
  2.3792760000E+00   5.1578880000E-02  -1.8876630000E-01
  8.8583900000E-01   2.7076110000E-01   1.0151990000E-01
  1.2852900000E-01  -1.1247700000E+00   9.7909060000E-01
0 1 1 0.0 1.0   
  4.5195000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 8.0 1.0   
  2.8191470000E+01   9.0988810000E-02   
  7.5235840000E+00   3.9582080000E-01   
  2.2712280000E+00   6.9471540000E-01   
0 3 1 0.0 1.0   
  6.1160300000E-01   1.0000000000E+00   
0 4 1 0.0 1.0   
  8.0000000000E-01   1.0000000000E+00   

29  8
0 0 6 2.0 1.00   
  7.6794380000E+04   1.7481610000E-03   
  1.1530700000E+04   1.3396020000E-02   
  2.6265750000E+03   6.6108850000E-02   
  7.4049030000E+02   2.2982650000E-01   
  2.3735280000E+02   4.7876750000E-01   
  8.1158180000E+01   3.5307390000E-01   
0 1 6 8.0 1.0   
  1.6108140000E+03   2.3640550000E-03   3.9633070000E-03
  3.8363670000E+02   3.1536350000E-02   3.1102230000E-02
  1.2417330000E+02   1.2694520000E-01   1.3613500000E-01
  4.6746780000E+01  -2.2628400000E-02   3.4929140000E-01
  1.9065690000E+01  -6.1920800000E-01   4.6247800000E-01
  7.8715670000E+00  -4.5853930000E-01   2.0201020000E-01
0 1 6 8.0 1.0   
  6.4457320000E+01  -4.3310750000E-03  -7.5237250000E-03
  2.1852120000E+01   7.4123070000E-02  -2.9756870000E-02
  9.4053430000E+00   2.5421080000E-01   6.8496540000E-02
  3.9991680000E+00  -2.8748430000E-01   4.0271410000E-01
  1.6702970000E+00  -7.2914360000E-01   4.9084900000E-01
  6.5962700000E-01  -2.1139510000E-01   1.7592680000E-01
0 1 3 2.0 1.0   
  2.6000880000E+00   5.0275770000E-02  -1.7029110000E-01
  9.6309400000E-01   2.6500400000E-01   9.3101330000E-02
  1.3616100000E-01  -1.1201550000E+00   9.8143360000E-01
0 1 1 0.0 1.0   
  4.7332000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 9.0 1.0   
  3.0853410000E+01   9.1999050000E-02   
  8.2649850000E+00   3.9850210000E-01   
  2.4953320000E+00   6.9178970000E-01   
0 3 1 0.0 1.0   
  6.6765800000E-01   1.0000000000E+00   
0 4 1 0.0 1.0   
  8.0000000000E-01   1.0000000000E+00   

30  8
0 0 6 2.0 1.00   
  8.2400940000E+04   1.7433290000E-03   
  1.2372550000E+04   1.3359660000E-02   
  2.8183510000E+03   6.5943650000E-02   
  7.9457170000E+02   2.2941510000E-01   
  2.5472320000E+02   4.7854530000E-01   
  8.7138800000E+01   3.5377530000E-01   
0 1 6 8.0 1.0   
  1.7325690000E+03   2.3614590000E-03   3.9631250000E-03
  4.1271490000E+02   3.1501770000E-02   3.1134110000E-02
  1.3367800000E+02   1.2727740000E-01   1.3639310000E-01
  5.0385850000E+01  -2.1459280000E-02   3.5012660000E-01
  2.0583580000E+01  -6.1976520000E-01   4.6231790000E-01
  8.5059400000E+00  -4.5901800000E-01   2.0049950000E-01
0 1 6 8.0 1.0   
  6.9364920000E+01  -4.4400980000E-03  -7.6892620000E-03
  2.3620820000E+01   7.5052530000E-02  -2.9979820000E-02
  1.0184710000E+01   2.5331110000E-01   7.0824110000E-02
  4.3340820000E+00  -2.8818970000E-01   4.0461410000E-01
  1.8109180000E+00  -7.2670520000E-01   4.8823250000E-01
  7.1484100000E-01  -2.1334390000E-01   1.7519700000E-01
0 1 3 2.0 1.0   
  2.8238420000E+00   4.8985430000E-02  -1.5867630000E-01
  1.0395430000E+00   2.5927930000E-01   8.3793270000E-02
  1.4326400000E-01  -1.1157110000E+00   9.8405470000E-01
0 1 1 0.0 1.0   
  4.9296000000E-02   1.0000000000E+00   1.0000000000E+00
0 3 3 10.0 1.0   
  3.3707640000E+01   9.2626480000E-02   
  9.0611060000E+00   4.0029800000E-01   
  2.7383830000E+00   6.8966080000E-01   
0 3 1 0.0 1.0   
  7.3029400000E-01   1.0000000000E+00   
0 4 1 0.0 1.0   
  8.0000000000E-01   1.0000000000E+00   


The 6-31G(d) Gaussian-Type Basis Sets

Use the 6-31G Hydrogen result and the 6-31G(d,p) “Other Atoms” result. Simple!


References

1. EMSL Basis Set Exchange: “The Role of Databases in Support of Computational Chemistry Calculations.” Feller, D., J. Comp. Chem., 17(13), 1571-1586, 1996.

2. “Basis Set Exchange: A Community Database for Computational Sciences.” Schuchardt, K.L., Didier, B.T., Elsethagen, T., Sun, L., Gurumoorthi, V., Chase, J., Li, J., and Windus, T.L. J. Chem. Inf. Model., 47(3), 1045-1052, 2007, doi:10.1021/ci600510j.

3. From EMSL: H – He: W.J. Hehre, R. Ditchfield and J.A. Pople, J. Chem. Phys. 56; Li – Ne: 2257 (1972). Note: Li and B come from J.D. Dill and J.A. Pople, J. Chem. Phys. 62, 2921 (1975); He is reportedly an unpublished basis set taken from Gaussian.

4. From EMSL: Na – Ar: M.M. Francl, W.J. Petro, W.J. Hehre, J.S. Binkley, M.S. Gordon, D.J. DeFrees and J.A. Pople, J. Chem. Phys. 77, 3654 (1982); Ne is reportedly an unpublished basis set taken from Gaussian.

5. From EMSL: K – Zn: V. Rassolov, J.A. Pople, M. Ratner and T.L. Windus, J. Chem. Phys. 109, 1223 (1998)

6. CRYSTAL09: R. Dovesi, R. Orlando, B. Civalleri, C. Roetti, V.R. Saunders, C.M. Zicovich-Wilson CRYSTAL: a computational tool for the ab initio study of the electronic properties of crystals Z. Kristallogr.220, 571–573 (2005).

7. CRYSTAL09: R. Dovesi, V.R. Saunders, C. Roetti, R. Orlando, C. M. Zicovich-Wilson, F. Pascale, B. Cival- leri, K. Doll, N.M. Harrison, I.J. Bush, Ph. D’Arco, M. Llunell CRYSTAL09 User’s Manual, University of Torino, Torino, 2009.

8. Gaussian09: Gaussian 09, Revision D.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2013.

9. B3LYP: A.D. Becke, J.Chem.Phys. 98 (1993) 5648-5652.

10. B3LYP: C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37 (1988) 785-789.

11. B3LYP: S.H. Vosko, L. Wilk, M. Nusair, Can. J. Phys. 58 (1980) 1200-1211.

12. B3LYP: P.J. Stephens, F.J. Devlin, C.F. Chabalowski, M.J. Frisch, J. Phys. Chem. 98 (1994) 11623-11627.

GROMACS 5.0.1, nVidia CUDA Toolkit, And FFTW3 Under Ubuntu 14.04 LTS (64-bit); The Virtues Of VirtualBox

Monday, September 22nd, 2014

Summarized below are the catches and fixes from a recent effort to build GROMACS 5.0.1 with FFTW3 (single- and double-precision) and GPU support (so, single-precision). Also, a trick I’ve been doing with great success lately, using a virtual machine to keep my real machine as clean as possible.

0. The Virtues Of VirtualBox

Open source means never having to say you’re sorry.

I’ve made the above proclamation to anyone who’d listen lately who has any interest in using Linux software (because, regardless of what anyone says on the matter, it ain’t there yet as an operating system for general scientific users with general computing know-how). You will very likely find yourself stuck at a configure or make step in one or more prerequisite codes to some final build you’re trying to do, leaving yourself to google error messages to try to come up with some kind of solution. Invariably, you’ll try something that seems to work, only to find it doesn’t, potentially leaving a trail of orphaned files, version-breaking changes, and random downgrading only to find something else stupid (or not) fixed your build problems.

I’ve an install I’m quite happy with that has all of the working code I want on it working – and I’ve no interest in having to perform re-installs to get back to a working state again.

My solution, which I’ve used to great success with GAMESS-US, GROMACS, NWChem, and Amber (so far), is to break a virtual instance in VirtualBox first. For those who don’t know (and briefly), VirtualBox lets you install a fully-working OS inside of your own OS that simply sits as a file in a Virtual VM folder in your user directory. My procedure has been to install a 60 GB VirtualBox instance of (currently) Ubuntu 14.04 (which I will refer to here as PROTOTYPE), fully update it to the current state of my RealBox (updates, upgrades, program installs, etc.), then copy PROTOTYPE somewhere else on the machine. The only limitation of this approach is that VirtualBox doesn’t give you access to the GPU if you’re testing CUDA-specific calculations. That said, it does let you install the CUDA Development Toolkit and compile code just fine, so you can at least work your way through a full build to make sure you don’t run into problems.

When you’re done trashing your VirtualBox after a particularly heinous build, just delete PROTOTYPE from Virtual VM and re-copy your copy back into Virtual VM – voila! You’re ready for another build operation (or to make sure your “final” build actually works flawlessly before committing the build to your RealBox.

That’s all I have to say on the matter. Consider it as your default procedure (at this point, I won’t touch my RealBox with new installs until I know it’s safe in VirtualBox).

1. The State Of My Machine Pre-GROMACS And All Other apt-get’s Used Below

What follows below is pretty straightforward. Errors you might get that don’t appear below might be related to the lack of certain installs on your machine that I installed on VirtualBox. That is, my standard PROTOTYPE comes standard with Intel’s Fortran and C Compilers (for code optimization). Those installs required a few installs above the base Ubuntu install. These are (and are pretty standard anyway, so I say install them anyway):

sudo apt-get install build-essential gcc-multilib rpm openjdk-7-jre-headless 

I could have just installed a fresh version of 14.04 onto a machine to try this myself, but I’m not that motivated. Also, note this list does not include the all-important cmake. We’ll get to that.

And for the rest of GROMACS (at least for older versions), there were lots of mesa/gnuplot/motif-specific dependencies in older versions of GROMACS to build all of the files included in the GROMACS package. Regardless of GPU builds or not, I tend to default to install all the packages below just to have them (which all, for 14.04, currently apt-get properly).

sudo apt-get install openmpi-bin openmpi-common gfortran csh grace menu x11proto-print-dev motif-clients freeglut3-dev libx11-dev libxmu-dev libxi-dev libgl1-mesa-glx libglu1-mesa libglu1-mesa-dev libgl1-mesa-dri libcurl-ocaml-dev libcurl4-gnutls-dev gnuplot

If you don’t install the libblas3gf libblas-doc libblas-dev liblapack3gf liblapack-doc liblapack-dev series, you’ll see the following note from your cmake steps in GROMACS.

— A library with BLAS API not found. Please specify library location.
— Using GROMACS built-in BLAS.
— LAPACK requires BLAS
— A library with LAPACK API not found. Please specify library location.
— Using GROMACS built-in LAPACK.

My own preference is to use the (assumedly newer) Ubuntu-specific libraries from apt-get.

sudo apt-get install libblas3gf libblas-doc libblas-dev liblapack3gf liblapack-doc liblapack-dev

GPU-Specific? One More apt-get

My first passes at proper GPU compilation involved several steps for the nVidia Developer Toolkit install. That’s now taken care of with apt-get, so perform the final apt-get to complete the component/dependency installations.

sudo apt-get install nvidia-cuda-dev nvidia-cuda-toolkit

With luck, your first attempt at a GPU-based installation will look like the following:

[0%] Building NVCC (Device) object src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o

[100%] Building CXX object src/programs/CMakeFiles/gmx.dir/legacymodules.cpp.o
Linking CXX executable ../../bin/gmx
[100%] Built target gmx

2. Nothing Happens Without cmake

Install cmake! Reproducing the output below to make sure you’re using the same versions for everything (in the event something breaks in the future).

sudo apt-get install cmake

Reading package lists… Done
Building dependency tree
Reading state information… Done
The following packages were automatically installed and are no longer required:
linux-headers-3.13.0-32 linux-headers-3.13.0-32-generic
linux-image-3.13.0-32-generic linux-image-extra-3.13.0-32-generic
Use ‘apt-get autoremove’ to remove them.
The following extra packages will be installed:
cmake-data
Suggested packages:
codeblocks eclipse
The following NEW packages will be installed:
cmake cmake-data
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 3,294 kB of archives.
After this operation, 16.6 MB of additional disk space will be used.
Do you want to continue? [Y/n]
Get:1 http://us.archive.ubuntu.com/ubuntu/ trusty/main cmake-data all 2.8.12.2-0ubuntu3 [676 kB]
Get:2 http://us.archive.ubuntu.com/ubuntu/ trusty/main cmake amd64 2.8.12.2-0ubuntu3 [2,618 kB]
Fetched 3,294 kB in 30s (106 kB/s)
Selecting previously unselected package cmake-data.
(Reading database … 258157 files and directories currently installed.)
Preparing to unpack …/cmake-data_2.8.12.2-0ubuntu3_all.deb …
Unpacking cmake-data (2.8.12.2-0ubuntu3) …
Selecting previously unselected package cmake.
Preparing to unpack …/cmake_2.8.12.2-0ubuntu3_amd64.deb …
Unpacking cmake (2.8.12.2-0ubuntu3) …
Processing triggers for man-db (2.6.7.1-1) …
Setting up cmake-data (2.8.12.2-0ubuntu3) …
Setting up cmake (2.8.12.2-0ubuntu3) …

3. First Pass At GROMACS

The make install step will place GROMACS where you want it on your machine, so you’re just as good building in $HOME/Downloads as you are anywhere else. I will be performing all operations from $HOME/Downloads unless otherwise stated.

According to the GROMACS Installation Manual, your quick-and-dirty install need only involve the following:

$ tar xvfz gromacs-src.tar.gz
$ ls
gromacs-src
$ mkdir build
$ cd build
$ cmake ../gromacs-src
$ make

This allows you build “out-of-source” as they put it. Frankly, I just dive right into the GROMACS folder and have at it.

CMake Error: The source directory “/home/user/Downloads/gromacs-5.0.1/build” does not appear to contain CMakeLists.txt.
Specify –help for usage, or press the help button on the CMake GUI.

And did you see the above error? If so, you read the GROMACS quick-and-dirty procedure backwards. I’m not running it this way, so doesn’t matter to what follows.

My first attempt at building GROMACS produced the following output from PROTOTYPE (reproducing all the text below).

user@PROTOTYPE:~$ cd Downloads/
user@PROTOTYPE:~/Downloads$ gunzip gromacs-5.0.1.tar.gz 
user@PROTOTYPE:~/Downloads$ tar xvf gromacs-5.0.1.tar 

gromacs-5.0.1/README
gromacs-5.0.1/INSTALL

gromacs-5.0.1/tests/CppCheck.cmake
gromacs-5.0.1/tests/CMakeLists.txt

user@PROTOTYPE:~/Downloads$ cd gromacs-5.0.1/
user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ cmake -DGMX_GPU=OFF

NOTE: If you just run cmake, you’ll get the following…

cmake version 2.8.12.2
Usage

cmake [options] cmake [options]

… which is to say, cmake requires at least one option be specified. Above, I’m just using -DGMX_GPU=OFF to start the process.

The C compiler identification is GNU 4.8.2
— The CXX compiler identification is GNU 4.8.2
— Check for working C compiler: /usr/bin/cc
— Check for working C compiler: /usr/bin/cc — works
— Detecting C compiler ABI info
— Detecting C compiler ABI info – done
— Check for working CXX compiler: /usr/bin/c++
— Check for working CXX compiler: /usr/bin/c++ — works
— Detecting CXX compiler ABI info
— Detecting CXX compiler ABI info – done
— Checking for GCC x86 inline asm
— Checking for GCC x86 inline asm – supported
— Detecting best SIMD instructions for this CPU
— Detected best SIMD instructions for this CPU – SSE2
— Try OpenMP C flag = [-fopenmp]
— Performing Test OpenMP_FLAG_DETECTED
— Performing Test OpenMP_FLAG_DETECTED – Success
— Try OpenMP CXX flag = [-fopenmp]
— Performing Test OpenMP_FLAG_DETECTED
— Performing Test OpenMP_FLAG_DETECTED – Success
— Found OpenMP: -fopenmp
— Performing Test CFLAGS_WARN
— Performing Test CFLAGS_WARN – Success
— Performing Test CFLAGS_WARN_EXTRA
— Performing Test CFLAGS_WARN_EXTRA – Success
— Performing Test CFLAGS_WARN_REL
— Performing Test CFLAGS_WARN_REL – Success
— Performing Test CFLAGS_WARN_UNINIT
— Performing Test CFLAGS_WARN_UNINIT – Success
— Performing Test CFLAGS_EXCESS_PREC
— Performing Test CFLAGS_EXCESS_PREC – Success
— Performing Test CFLAGS_COPT
— Performing Test CFLAGS_COPT – Success
— Performing Test CFLAGS_NOINLINE
— Performing Test CFLAGS_NOINLINE – Success
— Performing Test CXXFLAGS_WARN
— Performing Test CXXFLAGS_WARN – Success
— Performing Test CXXFLAGS_WARN_EXTRA
— Performing Test CXXFLAGS_WARN_EXTRA – Success
— Performing Test CXXFLAGS_WARN_REL
— Performing Test CXXFLAGS_WARN_REL – Success
— Performing Test CXXFLAGS_EXCESS_PREC
— Performing Test CXXFLAGS_EXCESS_PREC – Success
— Performing Test CXXFLAGS_COPT
— Performing Test CXXFLAGS_COPT – Success
— Performing Test CXXFLAGS_NOINLINE
— Performing Test CXXFLAGS_NOINLINE – Success
— Looking for include file unistd.h
— Looking for include file unistd.h – found
— Looking for include file pwd.h
— Looking for include file pwd.h – found
— Looking for include file dirent.h
— Looking for include file dirent.h – found
— Looking for include file time.h
— Looking for include file time.h – found
— Looking for include file sys/time.h
— Looking for include file sys/time.h – found
— Looking for include file io.h
— Looking for include file io.h – not found
— Looking for include file sched.h
— Looking for include file sched.h – found
— Looking for include file regex.h
— Looking for include file regex.h – found
— Looking for C++ include regex
— Looking for C++ include regex – not found
— Looking for posix_memalign
— Looking for posix_memalign – found
— Looking for memalign
— Looking for memalign – found
— Looking for _aligned_malloc
— Looking for _aligned_malloc – not found
— Looking for gettimeofday
— Looking for gettimeofday – found
— Looking for fsync
— Looking for fsync – found
— Looking for _fileno
— Looking for _fileno – not found
— Looking for fileno
— Looking for fileno – found
— Looking for _commit
— Looking for _commit – not found
— Looking for sigaction
— Looking for sigaction – found
— Looking for sysconf
— Looking for sysconf – found
— Looking for rsqrt
— Looking for rsqrt – not found
— Looking for rsqrtf
— Looking for rsqrtf – not found
— Looking for sqrtf
— Looking for sqrtf – not found
— Looking for sqrt in m
— Looking for sqrt in m – found
— Looking for clock_gettime in rt
— Looking for clock_gettime in rt – found
— Checking for sched.h GNU affinity API
— Performing Test sched_affinity_compile
— Performing Test sched_affinity_compile – Success
— Check if the system is big endian
— Searching 16 bit integer
— Looking for sys/types.h
— Looking for sys/types.h – found
— Looking for stdint.h
— Looking for stdint.h – found
— Looking for stddef.h
— Looking for stddef.h – found
— Check size of unsigned short
— Check size of unsigned short – done
— Using unsigned short
— Check if the system is big endian – little endian
— Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version “2.9.1”)
— Looking for xmlTextWriterEndAttribute in /usr/lib/x86_64-linux-gnu/libxml2.so
— Looking for xmlTextWriterEndAttribute in /usr/lib/x86_64-linux-gnu/libxml2.so – found
— Looking for include file libxml/parser.h
— Looking for include file libxml/parser.h – found
— Looking for include file pthread.h
— Looking for include file pthread.h – found
— Looking for pthread_create
— Looking for pthread_create – not found
— Looking for pthread_create in pthreads
— Looking for pthread_create in pthreads – not found
— Looking for pthread_create in pthread
— Looking for pthread_create in pthread – found
— Found Threads: TRUE
— Looking for include file pthread.h
— Looking for include file pthread.h – found
— Atomic operations found
— Performing Test PTHREAD_SETAFFINITY
— Performing Test PTHREAD_SETAFFINITY – Success
— Could NOT find Boost
Boost >= 1.44 not found. Using minimal internal version. This may cause trouble if you plan on compiling/linking other software that uses Boost against Gromacs.
— Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so
— Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so – found
— Setting build user/date/host/cpu information
— Setting build user & time – OK
— Checking floating point format
— Checking floating point format – IEEE754 (LE byte, LE word)
— Checking for 64-bit off_t
— Checking for 64-bit off_t – present
— Checking for fseeko/ftello
— Checking for fseeko/ftello – present
— Checking for SIGUSR1
— Checking for SIGUSR1 – found
— Checking for pipe support
— Checking for isfinite
— Performing Test isfinite_compile_ok
— Performing Test isfinite_compile_ok – Success
— Checking for isfinite – yes
— Checking for _isfinite
— Performing Test _isfinite_compile_ok
— Performing Test _isfinite_compile_ok – Failed
— Checking for _isfinite – no
— Checking for _finite
— Performing Test _finite_compile_ok
— Performing Test _finite_compile_ok – Failed
— Checking for _finite – no
— Performing Test CXXFLAG_STD_CXX0X
— Performing Test CXXFLAG_STD_CXX0X – Success
— Performing Test GMX_CXX11_SUPPORTED
— Performing Test GMX_CXX11_SUPPORTED – Success
— Checking for system XDR support
— Checking for system XDR support – present
— Try C compiler SSE2 flag = [-msse2]
— Performing Test C_FLAG_msse2
— Performing Test C_FLAG_msse2 – Success
— Performing Test C_SIMD_COMPILES_FLAG_msse2
— Performing Test C_SIMD_COMPILES_FLAG_msse2 – Success
— Try C++ compiler SSE2 flag = [-msse2]
— Performing Test CXX_FLAG_msse2
— Performing Test CXX_FLAG_msse2 – Success
— Performing Test CXX_SIMD_COMPILES_FLAG_msse2
— Performing Test CXX_SIMD_COMPILES_FLAG_msse2 – Success
— Enabling SSE2 SIMD instructions
— Performing Test _callconv___vectorcall
— Performing Test _callconv___vectorcall – Failed
— Performing Test _callconv___regcall
— Performing Test _callconv___regcall – Failed
— Performing Test _callconv_
— Performing Test _callconv_ – Success
— checking for module ‘fftw3f’
— package ‘fftw3f’ not found
— pkg-config could not detect fftw3f, trying generic detection
Could not find fftw3f library named libfftw3f, please specify its location in CMAKE_PREFIX_PATH or FFTWF_LIBRARY by hand (e.g. -DFFTWF_LIBRARY=’/path/to/libfftw3f.so’)
CMake Error at cmake/gmxManageFFTLibraries.cmake:76 (MESSAGE):
Cannot find FFTW 3 (with correct precision – libfftw3f for mixed-precision
GROMACS or libfftw3 for double-precision GROMACS). Either choose the right
precision, choose another FFT(W) library (-DGMX_FFT_LIBRARY), enable the
advanced option to let GROMACS build FFTW 3 for you
(-GMX_BUILD_OWN_FFTW=ON), or use the really slow GROMACS built-in fftpack
library (-DGMX_FFT_LIBRARY=fftpack).
Call Stack (most recent call first):
CMakeLists.txt:733 (include)

— Configuring incomplete, errors occurred!
See also “/home/user/Downloads/gromacs-5.0.1/CMakeFiles/CMakeOutput.log”.
See also “/home/user/Downloads/gromacs-5.0.1/CMakeFiles/CMakeError.log”.

Lots of little things to address here. We’ll get to the Boost problem later. Meantime, you can see the critical error is in (1) the lack of FFTW3 and (2) the lack of my specifically asking for -DGMX_BUILD_OWN_FFTW=ON in the cmake process.

NOTE: If you try to fix the FFTW3 problem as described above, you’ll get the following error:

-GMX_BUILD_OWN_FFTW=ON

CMake Error: Could not create named generator MX_BUILD_OWN_FFTW=ON

Make sure to put the “D” in:

-DGMX_BUILD_OWN_FFTW=ON

4. If You Don’t Use DGMX_BUILD_OWN_FFTW=ON To Build FFTW3…

This is a skip-able section if you’re letting cmake do the dirty work (and letting cmake do it is preferred, at least for getting GROMACS built). In trying sudo apt-get install fftw*, you see (currently) the following: fftw2 fftw-dev fftw-docs

No good. So, the procedure is to build FFTW3 from source (which is just as easy as installing from .deb or .rpm files if you installed everything I mentioned above). That said, your attempts to build FFTW3 and build GROMACS may have run into several errors because of how you built FFTW3. Beginning with your extracting and prep for make:

user@PROTOTYPE:~/Downloads$ tar xvf fftw-3.3.4.tar 
user@PROTOTYPE:~/Downloads$ cd fftw-3.3.4/

Any of the combinations below produce the same error:

user@PROTOTYPE:~/Downloads/fftw-3.3.4$ ./configure 
user@PROTOTYPE:~/Downloads/fftw-3.3.4$ ./configure -enable-shared=yes
user@PROTOTYPE:~/Downloads/fftw-3.3.4$ ./configure --enable-threads --enable-float

checking for a BSD-compatible install… /usr/bin/install -c
checking whether build environment is sane… yes

config.status: executing depfiles commands
config.status: executing libtool commands

user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ cmake -DGMX_GPU=OFF
user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ cmake -DGMX_GPU=OFF -DFFTWF_LIBRARY='/usr/local/lib/libfftw3.a'

— The C compiler identification is GNU 4.8.2
— The CXX compiler identification is GNU 4.8.2
— Check for working C compiler: /usr/bin/cc

— Performing Test PTHREAD_SETAFFINITY
— Performing Test PTHREAD_SETAFFINITY – Success
— Could NOT find Boost
Boost >= 1.44 not found. Using minimal internal version. This may cause trouble if you plan on compiling/linking other software that uses Boost against Gromacs.
— Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so
— Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so – found

— checking for module ‘fftw3f’
— package ‘fftw3f’ not found
— pkg-config could not detect fftw3f, trying generic detection
Could not find fftw3f library named libfftw3f, please specify its location in CMAKE_PREFIX_PATH or FFTWF_LIBRARY by hand (e.g. -DFFTWF_LIBRARY=’/path/to/libfftw3f.so’)
CMake Error at cmake/gmxManageFFTLibraries.cmake:76 (MESSAGE):
Cannot find FFTW 3 (with correct precision – libfftw3f for mixed-precision
GROMACS or libfftw3 for double-precision GROMACS). Either choose the right
precision, choose another FFT(W) library (-DGMX_FFT_LIBRARY), enable the
advanced option to let GROMACS build FFTW 3 for you
(-GMX_BUILD_OWN_FFTW=ON), or use the really slow GROMACS built-in fftpack
library (-DGMX_FFT_LIBRARY=fftpack).
Call Stack (most recent call first):
CMakeLists.txt:733 (include)

— Configuring incomplete, errors occurred!
See also “/home/user/Downloads/gromacs-5.0.1/CMakeFiles/CMakeOutput.log”.
See also “/home/user/Downloads/gromacs-5.0.1/CMakeFiles/CMakeError.log”.

Including –enable-shared takes care of this error and gets you to a successful GROMACS build.

user@PROTOTYPE:~/Downloads/fftw-3.3.4$ ./configure --enable-threads --enable-float --enable-shared

— The C compiler identification is GNU 4.8.2
— The CXX compiler identification is GNU 4.8.2
— Check for working C compiler: /usr/bin/cc

— Performing Test PTHREAD_SETAFFINITY
— Performing Test PTHREAD_SETAFFINITY – Success
— Could NOT find Boost
Boost >= 1.44 not found. Using minimal internal version. This may cause trouble if you plan on compiling/linking other software that uses Boost against Gromacs.
— Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so
— Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so – found

— checking for module ‘fftw3f’
— found fftw3f, version 3.3.4
— Looking for fftwf_plan_r2r_1d in /usr/local/lib/libfftw3f.so
— Looking for fftwf_plan_r2r_1d in /usr/local/lib/libfftw3f.so – found
— Looking for fftwf_have_simd_avx in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_simd_avx in /usr/local/lib/libfftw3f.so – not found
— Looking for fftwf_have_simd_sse2 in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_simd_sse2 in /usr/local/lib/libfftw3f.so – not found
— Looking for fftwf_have_simd_avx in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_simd_avx in /usr/local/lib/libfftw3f.so – not found
— Looking for fftwf_have_simd_altivec in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_simd_altivec in /usr/local/lib/libfftw3f.so – not found
— Looking for fftwf_have_simd_neon in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_simd_neon in /usr/local/lib/libfftw3f.so – not found
— Looking for fftwf_have_sse2 in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_sse2 in /usr/local/lib/libfftw3f.so – not found
— Looking for fftwf_have_sse in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_sse in /usr/local/lib/libfftw3f.so – not found
— Looking for fftwf_have_altivec in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_altivec in /usr/local/lib/libfftw3f.so – not found
CMake Warning at cmake/gmxManageFFTLibraries.cmake:89 (message):
The fftw library found is compiled without SIMD support, which makes it
slow. Consider recompiling it or contact your admin
Call Stack (most recent call first):
CMakeLists.txt:733 (include)

— Using external FFT library – FFTW3
— Looking for sgemm_

— Configuring done
— Generating done
— Build files have been written to: /home/user/Downloads/gromacs-5.0.1

And out of a first-pass GROMACS build…

user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ cmake -DGMX_GPU=OFF

Scanning dependencies of target libgromacs
[0%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/__/external/tng_io/src/compression/bwlzh.c.o
[0%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/__/external/tng_io/src/compression/bwt.c.o

[100%] Building CXX object src/programs/CMakeFiles/gmx.dir/legacymodules.cpp.o
Linking CXX executable ../../bin/gmx
[100%] Built target gmx

5. But You Let cmake Build FFTW3. So, Continuing The Build Process

With all of the dependencies above installed, the one note I wanted to address was that for Boost:


— Performing Test PTHREAD_SETAFFINITY – Success
— Could NOT find Boost
Boost >= 1.44 not found. Using minimal internal version. This may cause trouble if you plan on compiling/linking other software that uses Boost against Gromacs.
— Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so

It certainly isn’t a major issue, but I wanted to try to get an warning-free build. Installing Boost 1.56 produced the following negative result:

user@PROTOTYPE:~/Downloads/boost_1_56_0$ ./bootstrap.sh 

Building Boost.Build engine with toolset gcc… tools/build/src/engine/bin.linuxx86_64/b2
Detecting Python version… 2.7
Detecting Python root… /usr
Unicode/ICU support for Boost.Regex?… not found.
Generating Boost.Build configuration in project-config.jam…

Bootstrapping is done. To build, run:

./b2

To adjust configuration, edit ‘project-config.jam’.
Further information:

– Command line help:
./b2 –help

– Getting started guide:
http://www.boost.org/more/getting_started/unix-variants.html

– Boost.Build documentation:
http://www.boost.org/boost-build2/doc/html/index.html

user@PROTOTYPE:~/Downloads/boost_1_56_0$ sudo ./b2 install

Performing configuration checks

– 32-bit : no (cached)
– 64-bit : yes (cached)
– arm : no (cached)

…failed updating 58 targets…
…skipped 12 targets…
…updated 11322 targets…

user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ cmake -DGMX_GPU=ON -DGMX_DOUBLE=OFF
user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ make

[0%] Building NVCC (Device) object src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o
[0%] Building NVCC (Device) object src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o

[7%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o
In file included from /home/user/Downloads/gromacs-5.0.1/src/gromacs/options/basicoptions.h:52:0,
from /home/user/Downloads/gromacs-5.0.1/src/gromacs/commandline/cmdlinehelpwriter.cpp:55:
/home/user/Downloads/gromacs-5.0.1/src/gromacs/options/../utility/gmxassert.h:47:57: fatal error: boost/exception/detail/attribute_noreturn.hpp: No such file or directory
#include
^
compilation terminated.
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o] Error 1
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2

Sadly, the solution is to then include -DGMX_EXTERNAL_BOOST=off and stick with the internal boost, which then “makes” just fine. One page references the use of -DGMX_INTERNAL_BOOST=on, but that produced the following:

CMake Warning:
Manually-specified variables were not used by the project:

GMX_INTERNAL_BOOST

— Build files have been written to: /home/user/Downloads/gromacs-5.0.1

There’s more on this issue at: gerrit.gromacs.org/#/c/1232/ and t24960.science-biology-gromacs-development.biotalk.us/compiling-boost-problem-and-error-with-icc-t24960.html, but I’ve opted not to worry about it.

So, with Boost installed, I simply ignore it (and have not installed Boost on my RealBox).

user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ cmake -DGMX_GPU=ON -DGMX_EXTERNAL_BOOST=off

6. Finishing Step If All Above Goes Well: CUDA-Based GROMACS Build

If everything else above has gone smoothly (and if you ignored the Boost install. If you didn’t, remember to add -DGMX_EXTERNAL_BOOST=off to the cmake below), you should be able to cleanly run a cmake for a GPU version of GROMACS (below, with the final result to be placed into /opt/gromacs_gpu. You then specify the $PATH after and run with it).

user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ cmake -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs_gpu -DGMX_BUILD_OWN_FFTW=ON

— The C compiler identification is GNU 4.8.2
— The CXX compiler identification is GNU 4.8.2

— Generating done
— Build files have been written to: /home/damianallis/Downloads/gromacs-5.0.1

user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ make

The make starts with the FFTW3 download and build…

Scanning dependencies of target fftwBuild
[ 0%] Performing pre-download step for ‘fftwBuild’
— downloading…
src=’http://www.fftw.org/fftw-3.3.3.tar.gz’
dest=’/home/damianallis/Downloads/gromacs-5.0.1/src/contrib/fftw/fftw.tar.gz’
— [download 0% complete]

[100%] Building CXX object src/programs/CMakeFiles/gmx.dir/legacymodules.cpp.o
Linking CXX executable ../../bin/gmx
[100%] Built target gmx

Finally, your (sudo) make install places everything into /opt/gromacs_gpu.

user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ sudo make install

— The GROMACS-managed build of FFTW 3 will configure with the following optimizations: –enable-sse2
— Configuring done
— Generating done
— Build files have been written to: /home/damianallis/Downloads/gromacs-5.0.1
[1%] Built target fftwBuild

[100%] Building CXX object src/programs/CMakeFiles/gmx.dir/legacymodules.cpp.o
Linking CXX executable ../../bin/gmx
[100%] Built target gmx

For The Windows-Specific: Sed For Windows And A .bat File To Get Gaussian09 Files Working With aClimax

Wednesday, September 3rd, 2014

Provided you’ve installed Sed For Windows and know its proper path, the .bat file below should make all the modifications you need to your Gaussian09 .out files (in differently-named files at that) to get them properly loading in aClimax (see the previous post for all the details). A few simple steps:

1. Download and install Sed for Windows. Currently available at: gnuwin32.sourceforge.net/packages/sed.htm

2. Find its location on your machine. Under XP (where I’m using aClimax), this should be C:\Program Files\GnuWin32\bin

3. Copy + paste the text below into Notepad and save that as “aClimax_converter.bat” or something. NOTE: The quotes are IMPORTANT! You risk saving the file as an aClimax_converter.bat.txt file otherwise. The pause is optional. If there’s something wrong with the conversion, keeping the pause will let you see the error. If, by some miracle, your Sed is installed elsewhere, change the PATH statement below. The .aclimaxconversion_step1 file will be deleted (just there for doing sequential Sed’ing in case additional modifications are needed in the future).

PATH=C:\Program Files\GnuWin32\bin;
sed.exe "s/  Atom  AN/ Atom AN /g" %1 > %1.aclimaxconversion_step1
sed.exe "s/ Atom   / Atom/g" %1.aclimaxconversion_step1 > %1.aClimaxable.out
del %1.aclimaxconversion_step1
pause

4. If the path is right, just drag + drop your .out files onto the .bat file (with a shortcut to the .bat file, or place a copy of the file in your working directory).

5. Finally, try opening one of the .aClimaxeable.out files in aClimax and report back if you’ve any problems.

Obligatory

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