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Update to Milo 1.0.3
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@mteynor
mteynor committed Nov 18, 2021
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1,348 changes: 674 additions & 674 deletions LICENSE
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68 changes: 34 additions & 34 deletions README.md
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### Please cite Milo as:
Milo, Revision 1.0.2, M. S. Teynor, N. Wohlgemuth, L. Carlson, J. Huang, S. L. Pugh, B. O. Grant, R. S. Hamilton, R. Carlsen, and D. H. Ess, Brigham Young University, Provo UT, 2021.

### Requirements
#### Python:
Milo has only been tested against Python 3.8. It is expected to work with Python 3.6+, but will not work with Python 3.5 or older.

#### Gaussian:
Milo can interface with both Gaussian 16 and Gaussian 09 to perform force calculation. Milo expects Gaussian to be loaded as a module, as either "g16" for Gaussian 16 or "g09" for Gaussian 09.

#### Operating System:
Milo is only intended to work on a Linux based operating system through the command line.

### Installation Guide
1. Unzip milo-1.0.2.zip in your home directory
2. Add the following to your .bashrc:
`export PYTHONPATH=$PYTHONPATH:$HOME/milo-1.0.2`
3. (Optional) Also add the following to your .bashrc, to make calling scripts easier:
`export PATH=$PATH:$HOME/milo-1.0.2/milo_1_0_2/tools`
`module load python/3.8`
4. Source your .bashrc or restart your session.

You are now ready to run your first Milo job.

### Using Milo
To run a Milo job with Gaussian 16:
`module load python/3.8`
`module load g16`
`python -m milo_1_0_2 < job.in > job.out`

To run a Milo job with Gaussian 09:
`module load python/3.8`
`module load g09`
`python -m milo_1_0_2 < job.in > job.out`
### Please cite Milo as:
Milo, Revision 1.0.3, M. S. Teynor, N. Wohlgemuth, L. Carlson, J. Huang, S. L. Pugh, B. O. Grant, R. S. Hamilton, R. Carlsen, and D. H. Ess, Brigham Young University, Provo UT, 2021.

### Requirements
#### Python:
Milo has only been tested against Python 3.8. It is expected to work with Python 3.6+, but will not work with Python 3.5 or older.

#### Gaussian:
Milo can interface with both Gaussian 16 and Gaussian 09 to perform force calculation. Milo expects Gaussian to be loaded as a module, as either "g16" for Gaussian 16 or "g09" for Gaussian 09.

#### Operating System:
Milo is only intended to work on a Linux based operating system through the command line.

### Installation Guide
1. Unzip milo-1.0.3.zip in your home directory
2. Add the following to your .bashrc:
`export PYTHONPATH=$PYTHONPATH:$HOME/milo-1.0.3`
3. (Optional) Also add the following to your .bashrc, to make calling scripts easier:
`export PATH=$PATH:$HOME/milo-1.0.3/milo_1_0_3/tools`
`module load python/3.8`
4. Source your .bashrc or restart your session.

You are now ready to run your first Milo job.

### Using Milo
To run a Milo job with Gaussian 16:
`module load python/3.8`
`module load g16`
`python -m milo_1_0_3 < job.in > job.out`

To run a Milo job with Gaussian 09:
`module load python/3.8`
`module load g09`
`python -m milo_1_0_3 < job.in > job.out`
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98 changes: 49 additions & 49 deletions docs/vinyl_alcohol_example.in
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@@ -1,49 +1,49 @@
$job
gaussian_header m06 6-31g(d,p)
step_size 1.00
max_steps 100
temperature 298.15
phase bring_together 3 7
memory 24
processors 24
random_seed generate
$end
$molecule
0 1
C 1.200474 -0.217166 0.005312
H 2.140373 0.322623 0.057025
H 1.229644 -1.301649 -0.058870
C 0.047579 0.438089 0.007341
H 0.006491 1.530036 0.049096
O -1.172883 -0.178611 -0.110414
H -1.481767 -0.447660 0.760148
$end
$isotope
1 12.00000
2 1.00783
3 1.00783
4 12.00000
5 1.00783
6 15.99491
7 1.00783
$end
$frequency_data
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482.6444 2.1944 0.3012 0.15280 0.02762 -0.00072 -0.10925 0.49529 -0.00808 0.72285 0.04312 0.04838 0.00402 -0.20033 -0.00083 0.11275 -0.19094 -0.00473 -0.14914 0.09901 -0.00017 -0.22657 0.13759 -0.01446
695.5585 1.3254 0.3778 0.00107 -0.00235 0.03220 -0.03099 -0.01134 0.72199 0.04196 0.02776 -0.44882 0.00331 0.00052 -0.15641 0.00328 -0.01524 0.30098 -0.02132 -0.01067 0.04367 0.27193 0.18995 0.21170
891.2537 1.3611 0.6370 -0.00076 0.00699 -0.16945 -0.02583 -0.03426 0.71555 -0.00514 -0.04272 0.66491 -0.00354 0.00018 0.05685 0.00468 0.00553 -0.06946 0.00907 -0.00035 0.00355 -0.06652 -0.00829 -0.02660
952.7036 1.9153 1.0242 -0.18213 -0.09106 -0.00438 -0.55407 0.56242 -0.02924 0.49500 -0.05956 0.01882 -0.05486 0.00069 -0.01172 0.20515 0.01308 0.04767 0.16262 0.03519 0.01168 0.09476 0.00148 -0.03096
980.3828 1.0914 0.6181 0.00317 0.00235 0.00543 0.02508 -0.00777 -0.28773 -0.02140 -0.02932 0.51127 0.00461 0.00460 -0.08513 -0.01986 -0.03000 0.79321 -0.01227 -0.00069 -0.00695 0.11819 -0.00482 0.04248
1149.9397 2.0261 1.5786 -0.00374 -0.07273 -0.01432 -0.08971 0.11002 -0.09390 0.35685 -0.06467 0.07319 0.08597 0.15162 0.10428 0.27266 0.16442 -0.10035 -0.13837 -0.08878 -0.08134 0.67719 0.25981 0.34089
1235.6207 1.6208 1.4579 -0.01873 0.07168 -0.00653 -0.00836 0.03099 -0.07646 -0.38386 0.05709 0.05802 -0.06357 -0.17120 0.06609 -0.18116 -0.17310 -0.09807 0.05266 0.05813 -0.05501 0.71758 0.34749 0.28045
1327.1159 1.1186 1.1608 -0.02036 0.06769 0.00307 -0.11530 0.21117 0.01657 -0.44062 0.06366 -0.00853 0.03377 -0.04183 -0.00776 0.84930 -0.01157 0.02424 -0.02365 -0.03141 0.00317 -0.07760 -0.07267 -0.02678
1403.6059 1.2317 1.4297 0.04510 -0.06215 -0.00202 -0.35029 0.60774 0.03103 -0.51781 -0.06472 -0.01154 0.11240 0.02391 -0.00193 -0.45595 -0.00516 0.00098 -0.03007 -0.00352 0.00292 -0.07410 -0.02666 -0.01981
1738.0235 5.1967 9.2488 -0.35203 0.19150 0.00084 -0.08250 -0.41701 -0.01100 0.35876 0.28926 0.01289 0.44331 -0.14033 -0.00242 -0.36738 -0.26904 -0.01922 -0.05461 -0.01108 0.00424 -0.12907 -0.03659 -0.03122
3113.2425 1.0866 6.2048 0.00700 0.00097 0.00022 -0.13882 -0.08635 -0.00870 -0.00086 0.10245 0.00692 0.01042 -0.08363 -0.00287 -0.04714 0.97566 0.03583 -0.00121 -0.00015 -0.00060 -0.00138 -0.00519 0.00705
3160.0842 1.0687 6.2876 0.05715 -0.04183 -0.00124 -0.54176 -0.31896 -0.03028 -0.01660 0.75352 0.04508 -0.01195 0.01933 0.00057 0.01313 -0.16728 -0.00579 0.00028 -0.00005 0.00003 0.00269 0.00144 -0.00156
3260.9026 1.1169 6.9975 -0.05390 -0.08325 -0.00613 0.66065 0.37139 0.03577 -0.02726 0.63939 0.03837 0.00022 -0.00701 -0.00027 -0.00410 0.05790 0.00200 0.00053 0.00044 -0.00002 0.00143 -0.00095 0.00035
3904.2252 1.0668 9.5804 -0.00058 -0.00012 0.00008 -0.00144 -0.00018 0.00195 0.00051 0.00095 -0.00171 -0.00092 0.00008 -0.00110 -0.00223 -0.00864 -0.00222 0.02220 0.01854 -0.05562 -0.33141 -0.28593 0.89688
$end
$job
gaussian_header m06 6-31g(d,p)
step_size 1.00
max_steps 100
temperature 298.15
phase bring_together 3 7
memory 24
processors 24
random_seed generate
$end

$molecule
0 1
C 1.200474 -0.217166 0.005312
H 2.140373 0.322623 0.057025
H 1.229644 -1.301649 -0.058870
C 0.047579 0.438089 0.007341
H 0.006491 1.530036 0.049096
O -1.172883 -0.178611 -0.110414
H -1.481767 -0.447660 0.760148
$end

$isotope
1 12.00000
2 1.00783
3 1.00783
4 12.00000
5 1.00783
6 15.99491
7 1.00783
$end

$frequency_data
-429.7212 1.1336 0.1233 -0.00292 0.00889 -0.03109 0.00077 0.00556 -0.05316 -0.02203 0.01414 -0.10613 -0.00366 0.00475 0.04786 -0.00607 0.00297 0.18807 0.03616 -0.06491 -0.01976 -0.46819 0.84501 0.08511
482.6444 2.1944 0.3012 0.15280 0.02762 -0.00072 -0.10925 0.49529 -0.00808 0.72285 0.04312 0.04838 0.00402 -0.20033 -0.00083 0.11275 -0.19094 -0.00473 -0.14914 0.09901 -0.00017 -0.22657 0.13759 -0.01446
695.5585 1.3254 0.3778 0.00107 -0.00235 0.03220 -0.03099 -0.01134 0.72199 0.04196 0.02776 -0.44882 0.00331 0.00052 -0.15641 0.00328 -0.01524 0.30098 -0.02132 -0.01067 0.04367 0.27193 0.18995 0.21170
891.2537 1.3611 0.6370 -0.00076 0.00699 -0.16945 -0.02583 -0.03426 0.71555 -0.00514 -0.04272 0.66491 -0.00354 0.00018 0.05685 0.00468 0.00553 -0.06946 0.00907 -0.00035 0.00355 -0.06652 -0.00829 -0.02660
952.7036 1.9153 1.0242 -0.18213 -0.09106 -0.00438 -0.55407 0.56242 -0.02924 0.49500 -0.05956 0.01882 -0.05486 0.00069 -0.01172 0.20515 0.01308 0.04767 0.16262 0.03519 0.01168 0.09476 0.00148 -0.03096
980.3828 1.0914 0.6181 0.00317 0.00235 0.00543 0.02508 -0.00777 -0.28773 -0.02140 -0.02932 0.51127 0.00461 0.00460 -0.08513 -0.01986 -0.03000 0.79321 -0.01227 -0.00069 -0.00695 0.11819 -0.00482 0.04248
1149.9397 2.0261 1.5786 -0.00374 -0.07273 -0.01432 -0.08971 0.11002 -0.09390 0.35685 -0.06467 0.07319 0.08597 0.15162 0.10428 0.27266 0.16442 -0.10035 -0.13837 -0.08878 -0.08134 0.67719 0.25981 0.34089
1235.6207 1.6208 1.4579 -0.01873 0.07168 -0.00653 -0.00836 0.03099 -0.07646 -0.38386 0.05709 0.05802 -0.06357 -0.17120 0.06609 -0.18116 -0.17310 -0.09807 0.05266 0.05813 -0.05501 0.71758 0.34749 0.28045
1327.1159 1.1186 1.1608 -0.02036 0.06769 0.00307 -0.11530 0.21117 0.01657 -0.44062 0.06366 -0.00853 0.03377 -0.04183 -0.00776 0.84930 -0.01157 0.02424 -0.02365 -0.03141 0.00317 -0.07760 -0.07267 -0.02678
1403.6059 1.2317 1.4297 0.04510 -0.06215 -0.00202 -0.35029 0.60774 0.03103 -0.51781 -0.06472 -0.01154 0.11240 0.02391 -0.00193 -0.45595 -0.00516 0.00098 -0.03007 -0.00352 0.00292 -0.07410 -0.02666 -0.01981
1738.0235 5.1967 9.2488 -0.35203 0.19150 0.00084 -0.08250 -0.41701 -0.01100 0.35876 0.28926 0.01289 0.44331 -0.14033 -0.00242 -0.36738 -0.26904 -0.01922 -0.05461 -0.01108 0.00424 -0.12907 -0.03659 -0.03122
3113.2425 1.0866 6.2048 0.00700 0.00097 0.00022 -0.13882 -0.08635 -0.00870 -0.00086 0.10245 0.00692 0.01042 -0.08363 -0.00287 -0.04714 0.97566 0.03583 -0.00121 -0.00015 -0.00060 -0.00138 -0.00519 0.00705
3160.0842 1.0687 6.2876 0.05715 -0.04183 -0.00124 -0.54176 -0.31896 -0.03028 -0.01660 0.75352 0.04508 -0.01195 0.01933 0.00057 0.01313 -0.16728 -0.00579 0.00028 -0.00005 0.00003 0.00269 0.00144 -0.00156
3260.9026 1.1169 6.9975 -0.05390 -0.08325 -0.00613 0.66065 0.37139 0.03577 -0.02726 0.63939 0.03837 0.00022 -0.00701 -0.00027 -0.00410 0.05790 0.00200 0.00053 0.00044 -0.00002 0.00143 -0.00095 0.00035
3904.2252 1.0668 9.5804 -0.00058 -0.00012 0.00008 -0.00144 -0.00018 0.00195 0.00051 0.00095 -0.00171 -0.00092 0.00008 -0.00110 -0.00223 -0.00864 -0.00222 0.02220 0.01854 -0.05562 -0.33141 -0.28593 0.89688
$end
52 changes: 26 additions & 26 deletions docs/water_example.in
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$comment
Example input file for a simple quasiclassical trajectory of a water molecule.
$end
$job
step_size 1.00
max_steps 100
temperature 298
gaussian_header m062x 3-21g
$end
$molecule
0 1
O 0.00000000 0.00000000 0.11903700
H 0.00000000 0.75704900 -0.47614700
H 0.00000000 -0.75704900 -0.47614700
$end
$frequency_data
# Mode 1
1682.1354 1.0895 1.8163 -0.00000 0.00000 -0.07382 0.00000 0.39258 0.58580 0.00000 -0.39258 0.58580
# Mode 2
3524.4296 1.0389 7.6032 0.00000 -0.00000 0.04553 0.00000 0.60700 -0.36126 -0.00000 -0.60700 -0.36126
# Mode 3
3668.7401 1.0827 8.5864 -0.00000 -0.07070 -0.00000 0.00000 0.56106 -0.42745 0.00000 0.56106 0.42745
$end
$comment
Example input file for a simple quasiclassical trajectory of a water molecule.
$end

$job
step_size 1.00
max_steps 100
temperature 298
gaussian_header m062x 3-21g
$end

$molecule
0 1
O 0.00000000 0.00000000 0.11903700
H 0.00000000 0.75704900 -0.47614700
H 0.00000000 -0.75704900 -0.47614700
$end

$frequency_data
# Mode 1
1682.1354 1.0895 1.8163 -0.00000 0.00000 -0.07382 0.00000 0.39258 0.58580 0.00000 -0.39258 0.58580
# Mode 2
3524.4296 1.0389 7.6032 0.00000 -0.00000 0.04553 0.00000 0.60700 -0.36126 -0.00000 -0.60700 -0.36126
# Mode 3
3668.7401 1.0827 8.5864 -0.00000 -0.07070 -0.00000 0.00000 0.56106 -0.42745 0.00000 0.56106 0.42745
$end
0 milo_1_0_2/__init__.py → milo_1_0_3/__init__.py
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2 changes: 1 addition & 1 deletion milo_1_0_2/__main__.py → milo_1_0_3/__main__.py
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Expand Up @@ -2,6 +2,6 @@
# -*- coding: utf-8 -*-
"""Run Milo."""

from milo_1_0_2 import main
from milo_1_0_3 import main

main.main()
0 milo_1_0_2/atom.py → milo_1_0_3/atom.py
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