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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.

Generating Molecular Orbitals (And Visualizing Assorted Properties) With The Gaussian09 cubegen Utility

Saturday, June 7th, 2014

To begin, this post owes its existence to the efforts of Dr. Douglas Fox at Gaussian, Inc., who provided me with an alternative explanation of how the cubegen utility works. After much wailing and gnashing of teeth, I intend on taking Dr. Fox’s advice and asking Gaussian Support for assistance earlier in my endeavors. What follows below, I hope, will save you some significant frustration (and, given how little there is online that really describes the extra workings of cubegen in a clear and example’ed way, it is my expectation that this page appeared early in your search list).

What I wanted out of cubegen that I couldn’t figure out how to get:

The situation was simple. I wanted my molecule centered and bound within an arbitrarily-sized box (X,Z,Y) for making images and doing additional post-processing. Specifically, I wanted to be able to take many different molecules (from hydrogen gas to big biomolecules) defined within the same-sized box for layering and presentation (different boxes for each, but all the same size).

I am assuming for this that you’re using cubegen from a terminal (not within GaussView or the like) to produce .cub/.cube files for use in some kind of rendering-capable program (like VESTA or VMD) and that cubegen and formchk are in your PATH (either properly placed or by running the Gaussian install script). I’ll be demonstrating usage with benzene (C6H6) and the benzene cation (C6H6+).

1. The Checkpoint File

To extract any kind of data for making .cub/.cube files, you need a checkpoint file (.chk) from your run. This is performed by adding a %chk=FILENAME.chk line to the top of the input file (which, if you’re a Gaussian user, you likely already know). If you want additional properties cube’d, check the Gaussian Tech Document, specifically looking at the Pop keyword for most of the properties you’d want visualized (this data gets placed into the .chk file for .cub/.cube generation after the run). For the standard molecular orbitals, they’re already saved in the .chk file (or their coefficients, anyway).

For benzene.gjf:

%chk=benzene.chk
# b3lyp/6-31G(d,p)

Benzene

0 1
 C                  1.20809735    0.69749533   -0.00000000
 C                  0.00000000    1.39499067   -0.00000000
 C                 -1.20809735    0.69749533   -0.00000000
 C                 -1.20809735   -0.69749533   -0.00000000
 C                  0.00000000   -1.39499067   -0.00000000
 C                  1.20809735   -0.69749533   -0.00000000
 H                  2.16038781    1.24730049   -0.00000000
 H                  0.00000000    2.49460097   -0.00000000
 H                 -2.16038781    1.24730049   -0.00000000
 H                 -2.16038781   -1.24730049   -0.00000000
 H                  0.00000000   -2.49460097   -0.00000000
 H                  2.16038781   -1.24730049   -0.00000000

For benzenecation.gjf:

%chk=benzenecation.chk
# b3lyp/6-31G(d,p)

Benzene cation

1 2
 C                  1.20809735    0.69749533   -0.00000000
 C                  0.00000000    1.39499067   -0.00000000
 C                 -1.20809735    0.69749533   -0.00000000
 C                 -1.20809735   -0.69749533   -0.00000000
 C                  0.00000000   -1.39499067   -0.00000000
 C                  1.20809735   -0.69749533   -0.00000000
 H                  2.16038781    1.24730049   -0.00000000
 H                  0.00000000    2.49460097   -0.00000000
 H                 -2.16038781    1.24730049   -0.00000000
 H                 -2.16038781   -1.24730049   -0.00000000
 H                  0.00000000   -2.49460097   -0.00000000
 H                  2.16038781   -1.24730049   -0.00000000

2. Convert The .chk To .fchk With formchk

As per the Gaussian Tech Doc:

formchk converts the data in a Gaussian checkpoint file into a formatted form which is suitable for input into a variety of visualization software.

Basically, making the .chk file something that cubegen can manipulate to generate .cub/.cube files of orbitals, densities, electrostatic potentials, etc. This run is simple for most users (for the rest, see formchk).

formchk benzene.chk benzene.fchk
formchk benzenecation.chk benzenecation.fchk

3. Using cubegen

And now the fun begins. A typical cubegen run looks like the following:

cubegen 0 MO=HOMO benzene.fchk benzene_HOMO.cub 0 h

cubegen – run cubegen
0 – an old memory flag (must be there, but not important)
MO=HOMO – generate the highest occupied molecular orbital
benzene.fchk – the .fchk file
benzene_HOMO.cub – the generated .cub file
0 – use the default grid point specification (80*80*80 points total in the whole cube file)
h – write out the .cub file with headers

The output you find summarized in VESTA is below for this case.

DEFAULT:
OpenGL version: 2.1 INTEL-8.26.34
Video configuration: Intel HD Graphics 4000 OpenGL Engine
Maximum supported width and height of the viewport: 16384 x 16384
OpenGL depth buffer bit: 16

/Users/damianallis/benzene_HOMO_default_0.cub
====================================================================================
Title Benzene MO=HOMO
Dimensions 87 91 65

Lattice parameters

a b c alpha beta gamma
9.39704 9.82909 7.02078 90.0000 90.0000 90.0000

Unit-cell volume = 648.469273 Å^3

Total number of polygons and unique vertices on slices;
(1 0 0): 0 ( 0), 0 ( 0)
(0 1 0): 0 ( 0), 0 ( 0)
(0 0 1): 0 ( 0), 0 ( 0)
====================================================================================

====================================================================================
Title Benzene

Lattice type P
Space group name P 1
Space group number 1
Setting number 1

Lattice parameters

a b c alpha beta gamma
1.00000 1.00000 1.00000 90.0000 90.0000 90.0000

Unit-cell volume = 1.000000 Å^3

Structure parameters

x y z Occ. B Site Sym.
1 C C1 4.65450 6.23638 3.44640 1.000 1.000 1 –
2 C C2 5.86259 5.53889 3.44640 1.000 1.000 1 –
3 C C3 5.86259 4.14389 3.44640 1.000 1.000 1 –
4 C C4 4.65450 3.44640 3.44640 1.000 1.000 1 –
5 C C5 3.44640 4.14389 3.44640 1.000 1.000 1 –
6 C C6 3.44640 5.53889 3.44640 1.000 1.000 1 –
7 H H1 4.65450 7.33599 3.44640 1.000 1.000 1 –
8 H H2 6.81488 6.08869 3.44640 1.000 1.000 1 –
9 H H3 6.81488 3.59409 3.44640 1.000 1.000 1 –
10 H H4 4.65450 2.34679 3.44640 1.000 1.000 1 –
11 H H5 2.49411 3.59409 3.44640 1.000 1.000 1 –
12 H H6 2.49411 6.08869 3.44640 1.000 1.000 1 –
====================================================================================

Number of polygons and unique vertices on isosurface = 16904 (8460)
12 atoms, 12 bonds, 0 polyhedra; CPU time = 39 ms

For the coarse grid (-2) case:

cubegen 0 MO=HOMO benzene.fchk benzene_HOMO_default_m2.cub -2 h

The output you find summarized in VESTA is below for this case.

/Users/damianallis/benzene_HOMO_default_m2.cub
====================================================================================
Title Benzene MO=HOMO
Dimensions 54 56 40

Lattice parameters

a b c alpha beta gamma
9.52518 9.87796 7.05569 90.0000 90.0000 90.0000

Unit-cell volume = 663.865482 Å^3

Total number of polygons and unique vertices on slices;
(1 0 0): 0 ( 0), 0 ( 0)
(0 1 0): 0 ( 0), 0 ( 0)
(0 0 1): 0 ( 0), 0 ( 0)
====================================================================================

====================================================================================
Title Benzene

Lattice type P
Space group name P 1
Space group number 1
Setting number 1

Lattice parameters

a b c alpha beta gamma
1.00000 1.00000 1.00000 90.0000 90.0000 90.0000

Unit-cell volume = 1.000000 Å^3

Structure parameters

x y z Occ. B Site Sym.
1 C C1 4.65450 6.23638 3.44640 1.000 1.000 1 –
2 C C2 5.86259 5.53889 3.44640 1.000 1.000 1 –
3 C C3 5.86259 4.14389 3.44640 1.000 1.000 1 –
4 C C4 4.65450 3.44640 3.44640 1.000 1.000 1 –
5 C C5 3.44640 4.14389 3.44640 1.000 1.000 1 –
6 C C6 3.44640 5.53889 3.44640 1.000 1.000 1 –
7 H H1 4.65450 7.33599 3.44640 1.000 1.000 1 –
8 H H2 6.81488 6.08869 3.44640 1.000 1.000 1 –
9 H H3 6.81488 3.59409 3.44640 1.000 1.000 1 –
10 H H4 4.65450 2.34679 3.44640 1.000 1.000 1 –
11 H H5 2.49411 3.59409 3.44640 1.000 1.000 1 –
12 H H6 2.49411 6.08869 3.44640 1.000 1.000 1 –
====================================================================================

Number of polygons and unique vertices on isosurface = 6516 (3266)
12 atoms, 12 bonds, 0 polyhedra; CPU time = 10 ms

For the medium grid (-3) case:

cubegen 0 MO=HOMO benzene.fchk benzene_HOMO_default_m3.cub -3 h

The output you find summarized in VESTA is below for this case.

/Users/damianallis/benzene_HOMO_default_m3.cub
====================================================================================
Title Benzene MO=HOMO
Dimensions 107 111 79

Lattice parameters

a b c alpha beta gamma
9.43701 9.78980 6.96751 90.0000 90.0000 90.0000

Unit-cell volume = 643.703858 Å^3

Total number of polygons and unique vertices on slices;
(1 0 0): 0 ( 0), 0 ( 0)
(0 1 0): 0 ( 0), 0 ( 0)
(0 0 1): 0 ( 0), 0 ( 0)
====================================================================================

====================================================================================
Title Benzene

Lattice type P
Space group name P 1
Space group number 1
Setting number 1

Lattice parameters

a b c alpha beta gamma
1.00000 1.00000 1.00000 90.0000 90.0000 90.0000

Unit-cell volume = 1.000000 Å^3

Structure parameters

x y z Occ. B Site Sym.
1 C C1 4.65450 6.23638 3.44640 1.000 1.000 1 –
2 C C2 5.86259 5.53889 3.44640 1.000 1.000 1 –
3 C C3 5.86259 4.14389 3.44640 1.000 1.000 1 –
4 C C4 4.65450 3.44640 3.44640 1.000 1.000 1 –
5 C C5 3.44640 4.14389 3.44640 1.000 1.000 1 –
6 C C6 3.44640 5.53889 3.44640 1.000 1.000 1 –
7 H H1 4.65450 7.33599 3.44640 1.000 1.000 1 –
8 H H2 6.81488 6.08869 3.44640 1.000 1.000 1 –
9 H H3 6.81488 3.59409 3.44640 1.000 1.000 1 –
10 H H4 4.65450 2.34679 3.44640 1.000 1.000 1 –
11 H H5 2.49411 3.59409 3.44640 1.000 1.000 1 –
12 H H6 2.49411 6.08869 3.44640 1.000 1.000 1 –
====================================================================================

Number of polygons and unique vertices on isosurface = 25532 (12774)
12 atoms, 12 bonds, 0 polyhedra; CPU time = 51 ms

For the fine grid (-4) case:

cubegen 0 MO=HOMO benzene.fchk benzene_HOMO_default_m4.cub -4 h

The output you find summarized in VESTA is below for this case.

/Users/damianallis/benzene_HOMO_default_m4.cub
====================================================================================
Title Benzene MO=HOMO
Dimensions 212 221 157

Lattice parameters

a b c alpha beta gamma
9.34876 9.74564 6.92337 90.0000 90.0000 90.0000

Unit-cell volume = 630.786281 Å^3

Total number of polygons and unique vertices on slices;
(1 0 0): 0 ( 0), 0 ( 0)
(0 1 0): 0 ( 0), 0 ( 0)
(0 0 1): 0 ( 0), 0 ( 0)
====================================================================================

====================================================================================
Title Benzene

Lattice type P
Space group name P 1
Space group number 1
Setting number 1

Lattice parameters

a b c alpha beta gamma
1.00000 1.00000 1.00000 90.0000 90.0000 90.0000

Unit-cell volume = 1.000000 Å^3

Structure parameters

x y z Occ. B Site Sym.
1 C C1 4.65450 6.23638 3.44640 1.000 1.000 1 –
2 C C2 5.86259 5.53889 3.44640 1.000 1.000 1 –
3 C C3 5.86259 4.14389 3.44640 1.000 1.000 1 –
4 C C4 4.65450 3.44640 3.44640 1.000 1.000 1 –
5 C C5 3.44640 4.14389 3.44640 1.000 1.000 1 –
6 C C6 3.44640 5.53889 3.44640 1.000 1.000 1 –
7 H H1 4.65450 7.33599 3.44640 1.000 1.000 1 –
8 H H2 6.81488 6.08869 3.44640 1.000 1.000 1 –
9 H H3 6.81488 3.59409 3.44640 1.000 1.000 1 –
10 H H4 4.65450 2.34679 3.44640 1.000 1.000 1 –
11 H H5 2.49411 3.59409 3.44640 1.000 1.000 1 –
12 H H6 2.49411 6.08869 3.44640 1.000 1.000 1 –
====================================================================================

Number of polygons and unique vertices on isosurface = 100680 (50348)
12 atoms, 12 bonds, 0 polyhedra; CPU time = 155 ms

These all generate a file containing the highest occupied molecular orbital (or one of the degenerate HOMO’s in this case. Do I have to qualify that this doesn’t mean what 99.5% of the people coming to this page thinks this means?). The box is generated by something in cubegen to be 9.3ish x 9.7ish x 6.9ish Angstroms on a side and containing X points per Angstrom (and you can change the fineness of the grid points). The image below shows the four cases for the benzene HOMO. Click to see larger versions if you want to see the influence of grid fineness on the final image.

benzene_homo_gaussian_defaults_small

Click for a larger view.

Now, then, while the boxes are almost all identical, the same molecule and input gives four slightly different results. Fine for individual images, but not ideal for the obsessive-compulsive image maker. Also, you see how a box simply bounds the molecule, meaning no standardization of size if you needed that standardization for some reason.

   a        b        c       alpha    beta     gamma
 9.39704  9.82909  7.02078  90.0000  90.0000  90.0000 < - default (0)
 9.52518  9.87796  7.05569  90.0000  90.0000  90.0000 <- coarse (-2)
 9.43701  9.78980  6.96751  90.0000  90.0000  90.0000 <- medium (-3)
 9.34876  9.74564  6.92337  90.0000  90.0000  90.0000 <- fine (-4)

So, for a specific case - suppose I wanted this orbital in a box exactly 15 x 20 x 25 Angstroms on a side with the molecule offset from the center by -1.0 Angstrom in each direction.

I was pleased to finally discover that cubegen allows for that, although you have to ask Gaussian Support to find out how (until now, that is) and you need to do a little bit of math to get the placement right (or use the excel file I've linked in a .zip file found at 2014june7_cubegen_excel_file.xlsx).

You begin with the following:

cubegen 0 MO=HOMO benzene.fchk benzene_HOMO.cub -1 h

But for -1, Where do the numbers go?

From the Gaussian Tech Doc:

A value of -1 says to read the cube specification from the input stream, according to the following format:

IFlag, X0, Y0, Z0 Output unit number and initial point.
N1, X1, Y1, Z1 Number of points and step-size in the X-direction.
N2, X2, Y2, Z2 Number of points and step-size in the Y-direction.
N3, X3, Y3, Z3 Number of points and step-size in the Z-direction.

IFlag is the output unit number. If IFlag is less than 0, then a formatted file will be produced; otherwise, an unformatted file will be written.

Admittedly, “input stream” made no sense to me upon first and second read. I just knew that the program didn’t do anything when I ran it. Now obvious, this means you input the cube specifications by typing in (or, better, pasting in) the 16 numbers it asks for.

Continuing…

The -1 tells cubegen to “expect more input.” In this case, without explanation first, my input would look as below:

-12  -6.50000  -9.00000 -11.50000
 60   0.25000   0.00000   0.00000
 80   0.00000   0.25000   0.00000
100   0.00000   0.00000   0.25000

Which you just paste into your terminal at the new line (having pressed ENTER after typing out the cubegen line above).

How this works (and note the use of minus signs!):

-[# Atoms] -[Start Point For Box In X] -[Start Point For Box In Y] -[Start Point For Box In Z]
[Number of Points In X]   [Grid Fineness In X]   [Grid Fineness In Y]   [Grid Fineness In Z]
[Number of Points In Y]   [Grid Fineness In X]   [Grid Fineness In Y]   [Grid Fineness In Z]
[Number of Points In Y]   [Grid Fineness In X]   [Grid Fineness In Y]   [Grid Fineness In Z]

Assuming orthogonality in your box, the off-diagonals for the grid fineness matrix are zero.

-[# Atoms] -[Start Point For Box In X] -[Start Point For Box In Y] -[Start Point For Box In Z]
[Number of Points In X]  [Grid Fineness In X]   0.000   0.000
[Number of Points In Y]  0.000   [Grid Fineness In Y]   0.000
[Number of Points In Y]  0.000   0.000   [Grid Fineness In Z]

4. -6.5, -9, -11.5?

You build the box around your molecule in cubegen, which means you combine (1) where you want the molecule positions with (2) the number of grid points along each direction and (3) the fineness of the grid to generate the box. Here, I’m starting my hypothetical box at -6.5 in X, -9 in Y, and -11.5 in Z, then building out my molecule 121*.25 points in X, 161*.25 in Y, 201*.25 in Z. This will produce the intended box size with the molecule technically centered at the origin in the box (0,0,0), but the generation of all 121, 161, and 201 points in X, Y, and Z will result in the box going from -6.5 to 8.5, -9 to 11, and -11.5 to 13.5 (and there’s your asymmetry in the box). Alternatively, you could think of it as generating a box 15 x 20 x 25, then placing the center of the molecule at 6.5, 9, 11.5 (but you don’t specify the box size directly, instead relying on the relative position of the molecule and the fineness of the grid to determine the position (from which you could work back to get the number of points you needed in each direction if you knew the size of the box you wanted. Yes, you might have to re-read that a few times).

I demonstrate this below for a benzene orbital “walk” along X using direct output from VESTA. The rest of the numbers in my matrix above are the same except for the “-[Start Point For The Box In X]” value.

benzene_homo_walk

The benzene walk (numbers show the spacing based on the cubegen input above).

5. Formula For Boxes And Grid Points

You can, in fact, work from the box size you want and relative position of the molecule in that box with some simple math. That looks like the table below:

-(# Atoms)           -(X Position)  -(Y Position)  -(Z Position)
(Box Size / X Mesh)    X Mesh         0.00000        0.00000
(Box Size / Y Mesh)    0.00000        Y Mesh         0.00000
(Box Size / Z Mesh)    0.00000        0.00000        Z Mesh

You specify # Atoms, X Position, Y Position, Z Position, X Mesh, Y Mesh and Z Mesh, then decide on how big your box is going to be. Also, note that X Position, Y Position, Z Position all need to be 1/2 the size of your box if you want the molecule centered. A way to help force this is to force the molecule to have its center of mass shifted to the origin using Symm=COM in your input file.

As mentioned above, a simple excel file for performing this task is provided for download at 2014june7_cubegen_excel_file.xlsx.

6. Lastly, A Procedure For Scripting The Generation Of Many Orbitals

That first stone passed, everything about making custom .cub/.cube files finally made sense. But it lead to another problem. Suppose I want to generate many molecular orbitals. Does one have to paste in the IFlag…Z3 block each time?

Thankfully, this process can be scripted to automation as well, although it’s not just a matter of pasting IFlag…Z3 below each run of cubegen. Doing that produces the following…

Example:

This isn’t a cubegen problem, it’s a Linux issue with the interpretation of stdin. The cubegen script needs to be fed in the matrix in a file (say cubegen.dat if you always want the same .cub/.cube file generated) or via the use of an EOF call.

Cubegen.dat:

cubegen 0 MO=1 benzene.fchk benzene_MO1.cub -1 h < cubegen.dat
cubegen 0 MO=2 benzene.fchk benzene_MO2.cub -1 h < cubegen.dat
cubegen 0 MO=3 benzene.fchk benzene_MO3.cub -1 h < cubegen.dat
...

EOF

cubegen 0 MO=1 benzene.fchk benzene_MO1.cub -1 h << EOF
-12  -6.50000  -9.00000 -11.50000
 60   0.25000   0.00000   0.00000
 80   0.00000   0.25000   0.00000
100   0.00000   0.00000   0.25000
EOF
cubegen 0 MO=2 benzene.fchk benzene_MO2.cub -1 h << EOF
-12  -6.50000  -9.00000 -11.50000
 60   0.25000   0.00000   0.00000
 80   0.00000   0.25000   0.00000
100   0.00000   0.00000   0.25000
EOF
cubegen 0 MO=3 benzene.fchk benzene_MO3.cub -1 h << EOF
-12  -6.50000  -9.00000 -11.50000
 60   0.25000   0.00000   0.00000
 80   0.00000   0.25000   0.00000
100   0.00000   0.00000   0.25000
EOF
...

7. What’s The Deal With The Benzene Cation?

Nothing, except I saw a question in my perusing of cubegen problems and found one related to UHF wavefunctions. How do you render alpha spin orbitals and beta spin orbitals? The answer is you dig into the .log file for the orbital energies and count (to the best of my knowledge).

Benzene (21 alpha/beta-occupied)

 Alpha  occ. eigenvalues -- -10.18955 -10.18928 -10.18928 -10.18872 -10.18872
 Alpha  occ. eigenvalues -- -10.18845  -0.84761  -0.73971  -0.73971  -0.59595
 Alpha  occ. eigenvalues --  -0.59595  -0.51588  -0.45423  -0.43943  -0.41518
 Alpha  occ. eigenvalues --  -0.41518  -0.36090  -0.33862  -0.33862  -0.24750
 Alpha  occ. eigenvalues --  -0.24750
 Alpha virt. eigenvalues --   0.00266   0.00266   0.08636   0.14126   0.14126
 Alpha virt. eigenvalues --   0.16238   0.17957   0.17957   0.18681   0.29989
 Alpha virt. eigenvalues --   0.29989   0.31908   0.31908   0.46637   0.52628
 Alpha virt. eigenvalues --   0.54782   0.55099   0.56222   0.59294   0.60077
 Alpha virt. eigenvalues --   0.60077   0.60084   0.60084   0.62384   0.62384
 Alpha virt. eigenvalues --   0.66653   0.66653   0.74180   0.81178   0.81178
 Alpha virt. eigenvalues --   0.82134   0.83694   0.83694   0.91676   0.93745
 Alpha virt. eigenvalues --   0.93745   0.95812   1.08054   1.08054   1.12992
 Alpha virt. eigenvalues --   1.12992   1.20098   1.26111   1.30051   1.40786
 Alpha virt. eigenvalues --   1.40786   1.42585   1.42585   1.42914   1.42914
 Alpha virt. eigenvalues --   1.74102   1.76078   1.80542   1.87583   1.90680
 Alpha virt. eigenvalues --   1.90680   1.97195   1.97195   1.97924   1.97924
 Alpha virt. eigenvalues --   2.02762   2.07664   2.07664   2.29609   2.29609
 Alpha virt. eigenvalues --   2.34429   2.34429   2.35491   2.39944   2.40328
 Alpha virt. eigenvalues --   2.40328   2.44636   2.44636   2.48731   2.48731
 Alpha virt. eigenvalues --   2.50802   2.58538   2.58538   2.60300   2.65987
 Alpha virt. eigenvalues --   2.75521   2.80103   2.80103   3.03123   3.03123
 Alpha virt. eigenvalues --   3.18490   3.20485   3.21867   3.21867   3.37166
 Alpha virt. eigenvalues --   3.48298   3.48298   3.93339   4.13215   4.16289
 Alpha virt. eigenvalues --   4.16289   4.43754   4.43754   4.82384

RHF wave functions are easy as the alpha and beta spin orbitals are identical (so you just call one).

Benzene Cation (21 alpha occ, 20 beta occ)

 Alpha  occ. eigenvalues --  -10.44746 -10.44745 -10.44690 -10.44689 -10.41307
 Alpha  occ. eigenvalues --  -10.41306  -1.09893  -0.99649  -0.97270  -0.83278
 Alpha  occ. eigenvalues --   -0.83268  -0.74423  -0.68358  -0.67574  -0.65278
 Alpha  occ. eigenvalues --   -0.63494  -0.61047  -0.56837  -0.56618  -0.51141
 Alpha  occ. eigenvalues --   -0.47878
 Alpha virt. eigenvalues --   -0.25225  -0.22671  -0.10624  -0.07758  -0.05310
 Alpha virt. eigenvalues --   -0.04280  -0.01821  -0.00871   0.00401   0.08260
 Alpha virt. eigenvalues --    0.08579   0.09642   0.10056   0.25206   0.29439
 Alpha virt. eigenvalues --    0.31399   0.31852   0.34121   0.36475   0.36906
 Alpha virt. eigenvalues --    0.37451   0.38343   0.38500   0.39459   0.40284
 Alpha virt. eigenvalues --    0.43576   0.45334   0.52549   0.60260   0.60770
 Alpha virt. eigenvalues --    0.61287   0.62929   0.64337   0.70989   0.71650
 Alpha virt. eigenvalues --    0.71731   0.74333   0.85713   0.86949   0.90112
 Alpha virt. eigenvalues --    0.90952   0.98816   1.00856   1.05831   1.15646
 Alpha virt. eigenvalues --    1.17792   1.17972   1.18789   1.20601   1.20854
 Alpha virt. eigenvalues --    1.49713   1.52475   1.57000   1.65756   1.66784
 Alpha virt. eigenvalues --    1.68337   1.73545   1.74011   1.74167   1.74723
 Alpha virt. eigenvalues --    1.80258   1.82880   1.84586   2.04024   2.06015
 Alpha virt. eigenvalues --    2.12117   2.12667   2.14025   2.17682   2.18940
 Alpha virt. eigenvalues --    2.19096   2.22084   2.22451   2.24748   2.25480
 Alpha virt. eigenvalues --    2.28544   2.35165   2.36888   2.39005   2.41062
 Alpha virt. eigenvalues --    2.52629   2.57091   2.57724   2.79730   2.80863
 Alpha virt. eigenvalues --    2.95189   2.99029   2.99731   3.01110   3.14403
 Alpha virt. eigenvalues --    3.25310   3.26537   3.70063   3.88553   3.90763
 Alpha virt. eigenvalues --    3.92953   4.18629   4.20462   4.58339
  Beta  occ. eigenvalues --  -10.44304 -10.44303 -10.44252 -10.44250 -10.41463
  Beta  occ. eigenvalues --  -10.41462  -1.08758  -0.97673  -0.97028  -0.82708
  Beta  occ. eigenvalues --   -0.82377  -0.74165  -0.67883  -0.67164  -0.64793
  Beta  occ. eigenvalues --   -0.63478  -0.57727  -0.56637  -0.56323  -0.47270
  Beta virt. eigenvalues --   -0.41639  -0.21435  -0.21139  -0.10438  -0.05496
  Beta virt. eigenvalues --   -0.05056  -0.04232  -0.01054  -0.00739   0.00754
  Beta virt. eigenvalues --    0.08748   0.08784   0.10027   0.10356   0.25410
  Beta virt. eigenvalues --    0.30875   0.31655   0.33033   0.34430   0.37599
  Beta virt. eigenvalues --    0.38243   0.38423   0.38827   0.38857   0.40471
  Beta virt. eigenvalues --    0.40510   0.45633   0.45687   0.53548   0.60543
  Beta virt. eigenvalues --    0.61003   0.61366   0.63303   0.64325   0.71163
  Beta virt. eigenvalues --    0.71910   0.72371   0.74501   0.86611   0.87153
  Beta virt. eigenvalues --    0.90721   0.90982   0.99163   1.02443   1.07028
  Beta virt. eigenvalues --    1.17547   1.18130   1.19642   1.19672   1.20955
  Beta virt. eigenvalues --    1.21374   1.51458   1.52709   1.57335   1.66396
  Beta virt. eigenvalues --    1.67580   1.68460   1.73895   1.74747   1.75260
  Beta virt. eigenvalues --    1.75568   1.80924   1.84865   1.84936   2.06229
  Beta virt. eigenvalues --    2.06582   2.12479   2.12665   2.14334   2.18350
  Beta virt. eigenvalues --    2.18883   2.19283   2.22289   2.22978   2.25783
  Beta virt. eigenvalues --    2.25938   2.29233   2.36212   2.37068   2.39062
  Beta virt. eigenvalues --    2.42549   2.53376   2.57824   2.57840   2.79980
  Beta virt. eigenvalues --    2.80952   2.95964   2.99101   2.99875   3.01115
  Beta virt. eigenvalues --    3.14561   3.25632   3.26592   3.70353   3.89317
  Beta virt. eigenvalues --    3.92008   3.93146   4.19813   4.20623   4.58989

In the case of UHF wave functions, you specify alpha or beta using AMO= or BMO= when you run cubegen.

Compiling And Running GAMESS-US (1 May 2013(R1)) On 64-bit Ubuntu 12.X/13.X In SMP Mode

Saturday, April 5th, 2014

Author’s Note 1: It is my standard policy to put too much info into guides so that those who are searching for specific problems they come across will find the offending text in their searches. With luck, your “build error” search sent you here.

Author’s Note 2: It’s not as bad as it looks (I’ve included lots of output and error messages for easy searching)!

Author’s Note 3: I won’t be much help for you in diagnosing your errors, but am happy to tweak the text below if something is unclear.

Conventions: I include both the commands you type in your Terminal and some of the output from these commands, the output being where most of the errors appear that I work on in the discussion.

Input is formatted as below:

username – your username (check your prompt)
machinename – your hostname (type hostname or check your prompt)

Text you put in at the (also shown, so you see the directory structure) prompt (copy + paste should be fine)

Text you get out (for checking results and reproducing errors)

Having just recently downloaded the newest version of GAMESS-US (R1 2013), my first few passes at using it under Linux (specifically, Ubuntu 12.04) ran into a few walls that required some straightforward modifications and a little bit of system prep planning. As my first few passes before successful execution are likely the same exact problems you might have run into in your attempts to get GAMESS-US to run (after a successful compilation and linking), I’m posting my problems and solutions here.

Qualifier 1 – My concern at the moment has been to get GAMESS-US to run under 64-bit Ubuntu 12.04 on a multi-core board (ye olde symmetric multiprocessing (which I always called single multi-processor, or SMP)). While some answers may follow in what’s below, this post doesn’t cover MPI-specific builds (nothing through a router, that is). SMP is the only concern (which is to say, I likely won’t have good answers if you send along an MPI-specific question). Also, although I’m VERY interested in trying it, I’ve not yet attempted to build a GPU-capable version (but plan to in the near future).

Qualifier 2 – It is my standard policy to install apps into /opt, and my steps below will reflect that (specifically because there’s a permission issue that needs to be addressed when you first try to build components). You can default to whatever you like, but keep in mind my tweaks when you try to build your local copy.

So, with the qualifiers in mind…

1. Prepping The System (apt-get)

There are few things better than being able to apt-get everything you need to prep your machine for an install, and I’m pleased to report that the (current) process for putting the important files onto Ubuntu 12.X/13.X is easy. Assuming you’re not going the Intel / PGI / MKL route, you can do everything by installing gfortran (compiler, presently installing 4.4) and the blas and atlas math libraries.

username@machinename:~$ sudo apt-get install gfortran libblas-dev libatlas-base-dev

Note: your atlas libraries will be installed in /usr/lib64/atlas/ – this will matter when you run config.

After these finish, run the following to determine your installed gfortran version (will be asked for by the new GAMESS config)

username@machinename:~$ gfortran -dumpversion

GNU Fortran (Ubuntu 4.4.3-4ubuntu5.1) 4.4.3 Copyright (C) 2010 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING

4.4 And you’re ready for GAMESS.

2. Downloading GAMESS-US, Placing Into /opt, And Changing Permissions

First, obviously, get the GAMESS source (click on the red text).

After downloading, copy/move gamess-current.tar.gz into /opt

username@machinename:~$ cd ~/Downloads
username@machinename:~/Downloads$ sudo cp gamess-current.tar.gz /opt
username@machinename:~/Downloads$ cd /opt
username@machinename:/opt$ sudo gunzip gamess-cuerent.tar.gz
username@machinename:/opt$ sudo tar xvd gamess-current.tar

gamess/ gamess/gms-files.csh gamess/tools/ ... gamess/misc/count.code gamess/misc/vbdum.src gamess/Makefile.in

At this point, if you go through the config process and get to the point of building ddikick.x, you will get an error when you first try to run ./compddi

username@machinename:/opt/gamess/ddi$ sudo ./compddi >& compddi.log &
[1] 4622 -bash: compddi.log: Permission denied

The problem is with the permission of the entire gamess folder:

drwxr-xr-x  4 root        root              4096 2014-04-04 21:43 . drwxr-xr-x 22 root        root              4096 2013-12-27 16:17 .. drwxr-xr-x 14 1300 504              4096 2014-04-04 21:43 gamess -rw-r--r-- 1 root        root         198481920 2014-04-04 21:42 gamess-current.tar

Which you remedy before running into this error by changing the permissions:

username@machinename:/opt$ sudo chown -R username gamess

The next step is recommended when you run config, so I’m performing the step here to get it out of the way. With the atlas libraries installed, generate two symbolic links.

username@machinename:/opt$ cd /usr/lib64/atlas
username@machinename:/usr/lib64/atlas$ sudo ln -s libf77blas.so.3.0 libf77blas.so
username@machinename:/usr/lib64/atlas$ sudo ln -s libatlas.so.3.0 libatlas.so

And, at this point, you’re ready to run the new (well, new to me) config script that preps your system install.

3. Building GAMESS-US

Back to the GAMESS-US folder.

username@machinename:/usr/lib64/atlas$ cd /opt/gamess
username@machinename:/opt/gamess$ sudo ./config
This script asks a few questions, depending on your computer system, to set up compiler names, libraries, message passing libraries, and so forth. You can quit at any time by pressing control-C, and then . Please open a second window by logging into your target machine, in case this script asks you to 'type' a command to learn something about your system software situation. All such extra questions will use the word 'type' to indicate it is a command for the other window. After the new window is open, please hit to go on.

You can open that second window or blindly assume that what I include below is all you need.

[enter]

GAMESS can compile on the following 32 bit or 64 bit machines: axp64 - Alpha chip, native compiler, running Tru64 or Linux cray-xt - Cray's massively parallel system, running CNL hpux32 - HP PA-RISC chips (old models only), running HP-UX hpux64 - HP Intel or PA-RISC chips, running HP-UX ibm32 - IBM (old models only), running AIX ibm64 - IBM, Power3 chip or newer, running AIX or Linux ibm64-sp - IBM SP parallel system, running AIX ibm-bg - IBM Blue Gene (P or L model), these are 32 bit systems linux32 - Linux (any 32 bit distribution), for x86 (old systems only) linux64 - Linux (any 64 bit distribution), for x86_64 or ia64 chips AMD/Intel chip Linux machines are sold by many companies mac32 - Apple Mac, any chip, running OS X 10.4 or older mac64 - Apple Mac, any chip, running OS X 10.5 or newer sgi32 - Silicon Graphics Inc., MIPS chip only, running Irix sgi64 - Silicon Graphics Inc., MIPS chip only, running Irix sun32 - Sun ultraSPARC chips (old models only), running Solaris sun64 - Sun ultraSPARC or Opteron chips, running Solaris win32 - Windows 32-bit (Windows XP, Vista, 7, Compute Cluster, HPC Edition) win64 - Windows 64-bit (Windows XP, Vista, 7, Compute Cluster, HPC Edition) winazure - Windows Azure Cloud Platform running Windows 64-bit type 'uname -a' to partially clarify your computer's flavor. please enter your target machine name:

We’re doing a linux64 build, so type the following at the prompt:

linux64
Where is the GAMESS software on your system? A typical response might be /u1/mike/gamess, most probably the correct answer is /opt/gamess GAMESS directory? [/opt/gamess]

Who is this mike and where is my folder u1? We’ll get to that in rungms. For now, I’m installing in /opt, so the default directory is fine:

[enter]

Setting up GAMESS compile and link for GMS_TARGET=linux64 GAMESS software is located at GMS_PATH=/opt/gamess Please provide the name of the build locaation. This may be the same location as the GAMESS directory. GAMESS build directory? [/opt/gamess]

Fine as selected.

[enter]

Please provide a version number for the GAMESS executable. This will be used as the middle part of the binary's name, for example: gamess.00.x Version? [00]

Is this important? Maybe, if you plan on building multiple versions of GAMESS-US (you might want a GPU-friendly version, one with a different compiler, one with MPI, etc.). Number as you wish and remember the number when it comes to rungms. That said, the actual linking step seems to really want to produce a 01 version (we’ll get to that). Meantime, default value is fine.

[enter]

Linux offers many choices for FORTRAN compilers, including the GNU compiler set ('g77' in old versions of Linux, or 'gfortran' in current versions), which are included for free in Unix distributions. There are also commercial compilers, namely Intel's 'ifort', Portland Group's 'pgfortran', and Pathscale's 'pathf90'. The last two are not common, and aren't as well tested as the others. type 'rpm -aq | grep gcc' to check on all GNU compilers, including gcc type 'which gfortran' to look for GNU's gfortran (a very good choice), type 'which g77' to look for GNU's g77, type 'which ifort' to look for Intel's compiler, type 'which pgfortran' to look for Portland Group's compiler, type 'which pathf90' to look for Pathscale's compiler. Please enter your choice of FORTRAN:

We’re using gfortran (currently 4.4.3):

gfortran

gfortran is very robust, so this is a wise choice. Please type 'gfortran -dumpversion' or else 'gfortran -v' to detect the version number of your gfortran. This reply should be a string with at least two decimal points, such as 4.1.2 or 4.6.1, or maybe even 4.4.2-12. The reply may be labeled as a 'gcc' version, but it is really your gfortran version. Please enter only the first decimal place, such as 4.1 or 4.6:
4.4

Alas, your version of gfortran does not support REAL*16, so relativistic integrals cannot use quadruple precision. Other than this, everything will work properly. hit to continue to the math library setup.

If this was my biggest concern I’d be a happy quantum chemist. Obviously you can try to install other flavors of gfortran and, possibly, by the time you need the procedure I’m following, a newer version of gfortran will be apt-gotten.

[enter]

Linux distributions do not include a standard math library. There are several reasonable add-on library choices, MKL from Intel for 32 or 64 bit Linux (very fast) ACML from AMD for 32 or 64 bit Linux (free) ATLAS from www.rpmfind.net for 32 or 64 bit Linux (free) and one very unreasonable option, namely 'none', which will use some slow FORTRAN routines supplied with GAMESS. Choosing 'none' will run MP2 jobs 2x slower, or CCSD(T) jobs 5x slower. Some typical places (but not the only ones) to find math libraries are Type 'ls /opt/intel/mkl' to look for MKL Type 'ls /opt/intel/Compiler/mkl' to look for MKL Type 'ls /opt/intel/composerxe/mkl' to look for MKL Type 'ls -d /opt/acml*' to look for ACML Type 'ls -d /usr/local/acml*' to look for ACML Type 'ls /usr/lib64/atlas' to look for Atlas Enter your choice of 'mkl' or 'atlas' or 'acml' or 'none':
atlas

Where is your Atlas math library installed? A likely place is /usr/lib64/atlas Please enter the Atlas subdirectory on your system:

Our location is, in fact, /usr/lib64/atlas, so we type it in accordingly.

NOTE: If you don’t type anything but [enter] below, the script closes (/usr/lib64/atlas is listed as the expected location, but it is not defaulted by the script. You need to type it in.

/usr/lib64/atlas
 
The linking step in GAMESS assumes that a softlink exists within the system's /usr/lib64/atlas from libatlas.so to a specific file like libatlas.so.3.0 from libf77blas.so to a specific file like libf77blas.so.3.0 config can carry on for the moment, but the 'root' user should chdir /usr/lib64/atlas ln -s libf77blas.so.3.0 libf77blas.so ln -s libatlas.so.3.0 libatlas.so prior to the linking of GAMESS to a binary executable. Math library 'atlas' will be taken from /usr/lib64/atlas please hit to compile the GAMESS source code activator

The symbolic linking was performed before the GAMESS steps.

[enter]

gfortran -o /home/username/gamess/tools/actvte.x actvte.f unset echo Source code activator was successfully compiled. please hit to set up your network for Linux clusters.
[enter]

If you have a slow network, like Gigabit Ethernet (GE), or if you have so few nodes you won't run extensively in parallel, or if you have no MPI library installed, or if you want a fail-safe compile/link and easy execution, choose 'sockets' to use good old reliable standard TCP/IP networking. If you have an expensive but fast network like Infiniband (IB), and if you have an MPI library correctly installed, choose 'mpi'. communication library ('sockets' or 'mpi')?

Again, I’m not building an mpi-friendly version, so am using sockets.

sockets

64 bit Linux builds can attach a special LIBCCHEM code for fast MP2 and CCSD(T) runs. The LIBCCHEM code can utilize nVIDIA GPUs, through the CUDA libraries, if GPUs are available. Usage of LIBCCHEM requires installation of HDF5 I/O software as well. GAMESS+LIBCCHEM binaries are unable to run most of GAMESS computations, and are a bit harder to create due to the additional CUDA/HDF5 software. Therefore, the first time you run 'config', the best answer is 'no'! If you decide to try LIBCCHEM later, just run this 'config' again. Do you want to try LIBCCHEM? (yes/no):
no

Your configuration for GAMESS compilation is now in /home/username/gamess/install.info Now, please follow the directions in /home/username/gamess/machines/readme.unix username@machinename:~/gamess$

At this stage, you’re ready to build ddikick.x and continue with the compiling.

4. Build ddikick.x

username@machinename:/opt/gamess$ cd ddi
username@machinename:/opt/gamess/ddi$ sudo ./compddi >& compddi.log &

Will dump output into compddi.log (which will now work with the correct permissions).

username@machinename:/opt/gamess/ddi$ sudo mv ddikick.x ..
username@machinename:/opt/gamess/ddi$ cd ..
username@machinename:/opt/gamess$ sudo ./compall >& compall.log &

Feel free to follow along as compall.log dumps results. You’re also welcome to follow the readme.unix advice:

This takes a while, so go for coffee, or check the SF Giants web page.

Upon completion, the last step is to link the executable.

Now, it used to be the case that you specified the version number in the lked step. So, if you wanted to stick with the 00 version from the config file, you’d type

username@machinename:/opt/gamess$ sudo ./lked gamess 00 >& lked.log &

When you do that at present, you get

[1] 7626 username@machinename:/opt/gamess$ [1]+ Stopped sudo ./lked gamess 00 &>lked.log

This then leads you to use the lked call from the readme.unix file.

username@machinename:/opt/gamess$ sudo ./lked gamess 01 >& lked.log &

Which then produces lked.log and gamess.01.x.

Now, if you run with 00 again, you get a successful linking of gamess.00.x . Not sure why this happens, but the version number isn’t important so long as you specify the right one when you use rungms (so I’ve not diagnosed it further).

At this point, you have a gamess.00.x and/or gamess.01.x executable in your /opt/gamess folder:

30828747 2014-04-04 22:41 gamess.01.x

I’m going to ignore the 00 issue out of the config file and use the gamess.01.x executable.

We’re ready to run calculations and work through the next set of errors you’ll receive if you don’t properly modify files.

5. PATH Setting

First, we copy rungms to our home folder, then add /opt/gamess to the PATH:

username@machinename:/opt/gamess$ cp rungms ~/
username@machinename:/opt/gamess$ cd ~/
username@machinename:~$ nano .bashrc

Add the following to the bottom of .bashrc (or extend your PATH)

PATH=$PATH:/opt/gamess

Quit nano and source.

username@machinename:~$ source .bashrc
[OPTIONAL] username@machinename:~$ echo $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:.../opt/gamess:

6. rungms (Probably Why You’re Here)

If you just go blindly into a run, you’ll get the following error:

username@machinename:~$ ./rungms test.inp

----- GAMESS execution script 'rungms' ----- This job is running on host machinename under operating system Linux at Fri Apr 4 22:47:55 EDT 2014 Available scratch disk space (Kbyte units) at beginning of the job is df: `/scr/username': No such file or directory df: no file systems processed GAMESS temporary binary files will be written to /scr/username GAMESS supplementary output files will be written to /home/username/scr Copying input file test.inp to your run's scratch directory... cp test.inp /scr/username/test.F05 cp: cannot create regular file `/scr/username/test.F05': No such file or directory unset echo /u1/mike/gamess/gms-files.csh: No such file or directory.

As is obvious, rungms needs some modifying.

username@machinename:~$ nano rungms

Scroll down until you see the following:

set TARGET=sockets set SCR=/scr/$USER set USERSCR=~$USER/scr set GMSPATH=/u1/mike/gamess

Given that it’s just me on the machine, I tend to simplify this by making SCR and USERSCR the same directory, and I make them both /tmp. If you intend on keeping all of the files, you’ll need to make rungms specific for each run case. My only concerns are .dat and .log, so /tmp dumping is fine. Furthermore, we must change GMSPATH from how the ever-helpful Mike Schmidt (he got me through some early issues when I started my GAMESS-US adventure 15ish years ago. Won’t complain about his continued default-ed presence in the scripts) has it set up at Iowa to how we want it on our own machines (in my case, /opt/gamess)

set TARGET=sockets set SCR=/tmp set USERSCR=/tmp set GMSPATH=/opt/gamess

With these modifications, your next run will be a bit more successful:

username@machinename:~$ ./rungms test.inp

----- GAMESS execution script 'rungms' ----- This job is running on host machinename under operating system Linux at Fri Apr 4 22:51:35 EDT 2014 Available scratch disk space (Kbyte units) at beginning of the job is Filesystem 1K-blocks Used Available Use% Mounted on /dev/sda2 1905222596 249225412 1559217460 14% / GAMESS temporary binary files will be written to /tmp GAMESS supplementary output files will be written to /tmp Copying input file test.inp to your run's scratch directory... cp test.inp /tmp/test.F05 unset echo /opt/gamess/ddikick.x /opt/gamess/gamess.00.x test -ddi 1 1 machinename -scr /tmp Distributed Data Interface kickoff program. Initiating 1 compute processes on 1 nodes to run the following command: /opt/gamess/gamess.00.x test ****************************************************** * GAMESS VERSION = 1 MAY 2013 (R1) * * FROM IOWA STATE UNIVERSITY * * M.W.SCHMIDT, K.K.BALDRIDGE, J.A.BOATZ, S.T.ELBERT, * * M.S.GORDON, J.H.JENSEN, S.KOSEKI, N.MATSUNAGA, * * K.A.NGUYEN, S.J.SU, T.L.WINDUS, * * TOGETHER WITH M.DUPUIS, J.A.MONTGOMERY * * J.COMPUT.CHEM. 14, 1347-1363(1993) * **************** 64 BIT LINUX VERSION **************** ... INPUT CARD> DDI Process 0: shmget returned an error. Error EINVAL: Attempting to create 160525768 bytes of shared memory. Check system limits on the size of SysV shared memory segments. The file ~/gamess/ddi/readme.ddi contains information on how to display the current SystemV memory settings, and how to increase their sizes. Increasing the setting requires the root password, and usually a sytem reboot. DDI Process 0: error code 911 ddikick.x: application process 0 quit unexpectedly. ddikick.x: Fatal error detected. The error is most likely to be in the application, so check for input errors, disk space, memory needs, application bugs, etc. ddikick.x will now clean up all processes, and exit... ddikick.x: Sending kill signal to DDI processes. ddikick.x: Execution terminated due to error(s). unset echo ----- accounting info ----- Files used on the master node machinename were: -rw-r--r-- 1 username username 0 2014-04-04 22:51 /tmp/test.dat -rw-r--r-- 1 username username 1341 2014-04-04 22:51 /tmp/test.F05 ls: No match. ls: No match. ls: No match. Fri Apr 4 22:51:36 EDT 2014 0.0u 0.0s 0:01.08 9.2% 0+0k 0+8io 0pf+0w

Things worked, but with a memory error. This issue is discussed at the Baldridge Group wiki: ocikbapps.uzh.ch/kbwiki/gamess_troubleshooting.html

From the wiki:

If you are sure you are not asking for too much memory in the input file, check that your kernel parameters are not allowing enough memory to be requested. You might have to increase the SHMALL & SHMAX kernel memory values to allow GAMESS to run. (See http://www.pythian.com/news/245/the-mysterious-world-of-shmmax-and-shmall/ for a better explanation.)
For example, on a machine with 4GB of memory, you might add these to /etc/sysctl.conf:
# cat /etc/sysctl.conf | grep shm
kernel.shmmax = 3064372224
kernel.shmall = 748137
Then set the new settings like so:
# sysctl -p
Since they are in /etc/sysctl.conf, they will automatically be set each time the system is booted.

In our case, we modify sysctl.conf with the recommendations from the wiki:

username@machinename:~$ sudo nano /etc/sysctl.conf

Add the following to the bottom of the file:

kernel.shmmax = 3064372224 kernel.shmall = 748137

Save and exit.

username@machinename:~$ sudo sysctl -p

net.ipv4.ip_forward = 1 kernel.shmmax = 3064372224 kernel.shmall = 748137

These memory values will change depending on your system.

Now we empty the /tmp and rerun.

username@machinename:~$ rm /tmp/*
username@machinename:~$ ./rungms test.inp

If your input file is worth it’s salt, you’ll have successfully run your file on a single processor (single core, that is). If you run into additional memory errors, increase kernel.shmmax and kernel.shmall.

Now, onto the SMP part. My first attempt to run games in parallel (on 4 cores using version 00) produced the following error:

username@machinename:~$ rm /tmp/*
username@machinename:~$ ./rungms test.inp 00 4

----- GAMESS execution script 'rungms' ----- This job is running on host machinename under operating system Linux at Fri Apr 4 22:52:52 EDT 2014 Available scratch disk space (Kbyte units) at beginning of the job is Filesystem 1K-blocks Used Available Use% Mounted on /dev/sda2 1905222596 249225416 1559217456 14% / GAMESS temporary binary files will be written to /tmp GAMESS supplementary output files will be written to /tmp Copying input file test.inp to your run's scratch directory... cp test.inp /tmp/test.F05 unset echo I do not know how to run this node in parallel.

I tried a number of stupid things to get the run to work, finally settling on modifying the rungms file properly. To make gamess know how to run the node in parallel, we need only make the following changes to our rungms file.

username@machinename:~$ nano rungms

Scroll down until you find the section below:

# 2. This is an example of how to run on a multi-core SMP enclosure, # where all CPUs (aka COREs) are inside a -single- NODE. # At other locations, you may wish to consider some of the examples # that follow below, after commenting out this ISU specific part. if ($NCPUS > 1) then switch (`hostname`) case se.msg.chem.iastate.edu: case sb.msg.chem.iastate.edu: if ($NCPUS > 2) set NCPUS=4 set NNODES=1

The change is simple. We remove the cases for $NCPUS > 1 in the file and add the hostname of our linux box (and if you don’t know this or it’s not in your prompt, simply type hostname at the prompt first). We’ll disable the two cases listed and add our hostname to the case list.

# 2. This is an example of how to run on a multi-core SMP enclosure, # where all CPUs (aka COREs) are inside a -single- NODE. # At other locations, you may wish to consider some of the examples # that follow below, after commenting out this ISU specific part. if ($NCPUS > 1) then switch (`hostname`) case machinename: # case se.msg.chem.iastate.edu: # case sb.msg.chem.iastate.edu: if ($NCPUS > 2) set NCPUS=4 set NNODES=1

This gives you parallel functionality, but it’s still not using the machine resources (cores) correctly when I ask for anything more than 2 cores (always using only 2 cores).

[minor complaint]
Admittedly, I don’t immediately get the logic of this section as currently coded, as one cannot get more than 2 cores to work in this case given how the if statements are written (so far as I can see now. I will assume I am the one missing something but have not decided to ask about it, instead changing the rungms text to the following). You can check this yourself by running top in another window. This is the most simple modification, and assumes you want to run N number of cores each time. Clearly, you can make this more elegant than it is (my modification, that is). Meantime, I want to run 4 cores on this machine, so I change the section to reflect a 4-core board (and commented out much of this section).
[/complaint]

# 2. This is an example of how to run on a multi-core SMP enclosure, # where all CPUs (aka COREs) are inside a -single- NODE. # At other locations, you may wish to consider some of the examples # that follow below, after commenting out this ISU specific part. if ($NCPUS > 1) then switch (`hostname`) case machinename # case se.msg.chem.iastate.edu: # case sb.msg.chem.iastate.edu: # if ($NCPUS > 2) set NCPUS=2 # set NNODES=1 # set HOSTLIST=(`hostname`:cpus=$NCPUS) # breaksw # case machinename # case br.msg.chem.iastate.edu: if ($NCPUS >= 4) set NCPUS=4 set NNODES=1 set HOSTLIST=(`hostname`:cpus=$NCPUS) breaksw case machinename # case cd.msg.chem.iastate.edu: # case zn.msg.chem.iastate.edu: # case ni.msg.chem.iastate.edu: # case co.msg.chem.iastate.edu: # case pb.msg.chem.iastate.edu: # case bi.msg.chem.iastate.edu: # case po.msg.chem.iastate.edu: # case at.msg.chem.iastate.edu: # case sc.msg.chem.iastate.edu: # if ($NCPUS > 4) set NCPUS=4 # set NNODES=1 # set HOSTLIST=(`hostname`:cpus=$NCPUS) # breaksw # case ga.msg.chem.iastate.edu: # case ge.msg.chem.iastate.edu: # case gd.msg.chem.iastate.edu: # if ($NCPUS > 6) set NCPUS=6 # set NNODES=1 # set HOSTLIST=(`hostname`:cpus=$NCPUS) # breaksw default: echo I do not know how to run this node in parallel. exit 20 endsw endif #

And, with this set of changes, I’m using all 4 cores on the board (but have some significant memory issues when running MP2 calks. But that’s for another post).

The typical user will never be able to do what the GAMESS group has done in making an excellent program that also happens to be free. That said, the need to make changes to the rungms file is something that would be greatly simplified by having N number of rungms scripts for each case instead of a monolithic file that is mostly useless text to users not using one of the system types. This, for instance, would make rungms modification much easier. If I streamline rungms for my specific system, I may post a new file accordingly.

Experimental And Theoretical Studies Of Tetramethoxy-p-benzoquinone: Infrared Spectra, Structural And Lithium Insertion Properties

Friday, December 20th, 2013

Published earlier this year in RSC Advances (RSC Adv., 2013, 3, 19081-19096), a follow-up (for my part) to the study The Low-/Room-temperature Forms Of The Lithiated Salt Of 3,6-dihydroxy-2,5-dimethoxy-p-benzoquinone: A Combined Experimental And Dispersion-Corrected Density Functional Study in CrystEngComm last year. The theoretical section for this paper is a tour-de-force of Crystal09 solid-state optimizations, density functional and dispersion-correction dependence, and post-processing using Carlo Gotti’s TOPOND software. In brief, the combination of vibrational spectra, electochemical measurements, and solid-state density functional theory tests are used to predict the structure of the previously unknown lithiated tetramethoxy-p-benzoquinone structure based on the good-to-excellent agreement with two known TMQ crystal structures (the testing of density functionals and dispersion corrections being a very good survey of the pros and cons of the varied methods. If you were pondering an approach to follow to perform the same kind of theoretical analysis, the procedure set up by Gaëtan and Christine in this paper is fully worth your consideration).

2013dec20_rscadvances

Gaëtan Bonnard, Anne-Lise Barrès, Yann Danten, Damian G. Allis, Olivier Mentré, Daniele Tomerini, Carlo Gatti, Ekaterina I. Izgorodina, Philippe Poizot and Christine Frayret*

In the search for low-polluting electrode materials for batteries, the use of redox-active organic compounds represents a promising alternative to conventional metal-based systems. In this article we report a combined experimental and theoretical study of tetramethoxy-p-benzoquinone (TMQ). In carbonate-based electrolytes, electrochemical behaviour of this compound is characterized by a reversible insertion process located at approximately 2.85 V vs. Li+/Li0. This relatively high potential reactivity, coupled with our effort to develop computational methodologies in the field of organic electrode materials, prompted us to complement these experimental data with theoretical studies performed using density functional theory (DFT). Single crystals of TMQ were synthesized and thoroughly characterized showing that this quinonic species crystallised in the P21/n space group. The experimental crystal structure of TMQ was then used to assess various DFT methods. The structural features and vibrational spectra were thus predicted by using as a whole five common density functionals (PBE, LDA, revPBE, PBEsol, B3PW91) with and without a semi-empirical correction to account for the van der Waals interactions using either Grimme’s (DFT-D2) or Tkatchenko–Scheffler (TS) scheme. The most reliable combination of the DFT functional and the explicit dispersion correction was chosen to study the Li-intercalated molecular crystal (LiTMQ) with the view of indentifying Li insertion sites. A very close agreement with the experiment was found for the average voltage by using the most stable relaxed hypothetical LiTMQ structure. Additionally, a comparison of vibrational spectra gained either for TMQ molecule and its dimer in gas phase or through periodic calculation was undertaken with respect to the experimentally measured infrared spectra. The topological features of the bonds were also investigated in conjunction with estimates of net atomic charges to gain insight into the effect of chemical bonding and intermolecular interaction on Li intercalation. Finally, π-electron delocalization of both quinone and alkali salts of p-semiquinone were determined using the Harmonic Oscillator model of Aromaticity (HOMA) or aromatic fluctuation index (FLU) calculations.

Commensurate Urea Inclusion Crystals With The Guest (E,E)‐1,4-Diiodo-1,3-Butadiene

Friday, December 20th, 2013

Published in Crystal Growth & Design (Cryst. Growth Des., 2013, 13 (9), pp. 3852–3855) earlier this year. The theory work is less impressive than the successful crystal growth, with initial solid-state efforts in Crystal09 only very recently now producing good results (leaving the molecular calculations to Gaussian09 in this paper). The procedure leading to the observed crystal structure of this inclusion complex is a significant step in the direction of testing the theory proposed in Bond Alternation In Infinite Periodic Polyacetylene: Dynamical Treatment Of The Anharmonic Potential published earlier this year in J. Mol. Struct.

2013dec20_DIBD_UIC

Caption: Two views along the ba and ca crystal axes of the (E,E)‐1,4-Diiodo-1,3-Butadiene : Urea Inclusion Complex.

Amanda F. Lashua, Tiffany M. Smith, Hegui Hu, Lihui Wei, Damian G. Allis, Michael B. Sponsler, and Bruce S. Hudson

Abstract: The urea inclusion compound (UIC) with (E,E)-1,4-diiodo-1,3-butadiene (DIBD) as a guest (DIBD:UIC) has been prepared and crystallographically characterized at 90 and 298 K as a rare example of a commensurate, fully ordered UIC. The crystal shows nearly hexagonal channels in the monoclinic space group P21/n. The DIBD guest molecules are arranged end-to-end with the nonbonding iodine atoms in the van der Waals contact. The guest structure is compared with that for DIBD at 90 K and with computations for the periodic UIC and isolated DIBD molecule.

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