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Initial tests for writing functions #31

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merged 8 commits into from
Oct 28, 2023
Merged

Initial tests for writing functions #31

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690c7bb
Initial tests and future tests for writing functions
CalCraven Oct 9, 2023
0768bf6
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 9, 2023
49e297e
remove pdb and mol2 from precommit modifications
CalCraven Oct 9, 2023
cc8c21d
Added tests with new gaussian files
CalCraven Oct 9, 2023
831ad15
merge in main
CalCraven Oct 27, 2023
98fee8c
fixes to issue with resetting dihedral_angle to -180 if equivalently 180
CalCraven Oct 23, 2023
b2d219b
set output test angles to be -180
CalCraven Oct 23, 2023
6625bf0
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 27, 2023
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4 changes: 2 additions & 2 deletions .pre-commit-config.yaml
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Expand Up @@ -14,7 +14,7 @@ repos:
- id: check-yaml
- id: end-of-file-fixer
- id: trailing-whitespace
exclude: '^docs/|setup.cfg|\.txt$|\.log$|\.xyz$'
exclude: '^docs/|setup.cfg|\.txt$|\.log$|\.xyz$|\.pdb$|\.mol2$'
- repo: https://github.com/psf/black
rev: 23.10.0
hooks:
Expand All @@ -27,5 +27,5 @@ repos:
hooks:
- id: isort
name: isort (python)
exclude: '^docs/|setup.cfg|\.txt$|\.log$|\.xyz$'
exclude: '^docs/|setup.cfg|\.txt$|\.log$|\.xyz$|\.pdb$|\.mol2$'
args: [--profile=black, --line-length=80]
7 changes: 7 additions & 0 deletions mosdef_dihedral_fit/tests/base_test.py
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@@ -1,3 +1,5 @@
import pathlib

import numpy as np
import pytest

Expand All @@ -6,3 +8,8 @@ class BaseTest:
@pytest.fixture(autouse=True)
def initdir(self, tmpdir):
tmpdir.chdir()

def get_fn(self, pathname):
"""Get test file path in test/files"""
current_path = pathlib.Path(__file__).parent.resolve()
return str(current_path / "files" / pathname)
31,966 changes: 31,966 additions & 0 deletions mosdef_dihedral_fit/tests/files/CT_CT_C_OH_multiplicity_1.log
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40 changes: 40 additions & 0 deletions mosdef_dihedral_fit/tests/files/dihedral.txt
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# Scan of Total Energy
# X-Axis: Scan Coordinate
# Y-Axis: Total Energy (Hartree)
# X Y
-170.0 -79.2284584810
-160.0 -79.2276350548
-150.0 -79.2264707680
-140.0 -79.2252587144
-130.0 -79.2243392257
-120.0 -79.2239963440
-110.0 -79.2243396104
-100.0 -79.2252571229
-90.0 -79.2264671389
-80.0 -79.2276315942
-70.0 -79.2284577839
-60.0 -79.2287550063
-50.0 -79.2284577649
-40.0 -79.2276318383
-30.0 -79.2264681503
-20.0 -79.2252587599
-10.0 -79.2243404876
0.0 -79.2239966896
10.0 -79.2243404856
20.0 -79.2252587696
30.0 -79.2264681707
40.0 -79.2276317493
50.0 -79.2284577902
60.0 -79.2287550076
70.0 -79.2284577870
80.0 -79.2276316437
90.0 -79.2264671464
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110.0 -79.2243396623
120.0 -79.2239966359
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140.0 -79.2252591195
150.0 -79.2264709151
160.0 -79.2276351404
170.0 -79.2284591083
-180.0 -79.2287549865
9 changes: 9 additions & 0 deletions mosdef_dihedral_fit/tests/files/dihedral_coords_position_36.txt
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@@ -0,0 +1,9 @@
Row Highlight Display Tag Symbol X Y Z
1 No Show 1 C -0.0 0.763665 -6e-06
2 No Show 2 C -0.0 -0.763665 -6e-06
3 No Show 3 H -1.012181 1.156071 -4e-06
4 No Show 4 H 0.505895 1.156447 0.876552
5 No Show 5 H 0.505848 1.156531 -0.876509
6 No Show 6 H 1.012181 -1.156071 -4e-06
7 No Show 7 H -0.505895 -1.156447 0.876552
8 No Show 8 H -0.505848 -1.156531 -0.876509
54 changes: 54 additions & 0 deletions ...dihedral_fit/tests/files/gaussian/CT_CT_C_OH/input/CT_CT_C_OH_Gaussian_multiplicity_1.txt
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#!/bin/bash

#SBATCH --job-name 4c_m1_CT_CT_C_OH
#SBATCH -q primary
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --mem=32G
#SBATCH --constraint=intel
#SBATCH --mail-type=ALL
#SBATCH [email protected]
#SBATCH -o output_%j.out
#SBATCH -e errors_%j.err
#SBATCH -t 168:0:0

echo "Running on host" hostname
echo "Time is" date

source ~/.bashrc

module swap gnu7 intel/2019


JOB=CT_CT_C_OH_multiplicity_1
DIR=examples/protonated_fragment__CT_CT_C_OH/src/guassian_runs_multiplicity_1/CT_CT_C_OH_Gaussian_multiplicity_1.txt


g16<< EOF > $DIR/$JOB.log




%chk=$JOB.chk
%nproc=4
%mem=32GB
# opt=modredundant UHF/6-31G* SCF=(MaxCycle=1000) Geom=PrintInputOrient

Dihedral Scan at UHF/6-31G*

0 1
C 0.0000 0.0000 0.0000
C -1.5000 0.0000 0.0000
C -2.2000 1.2124 0.0000
O 0.7000 -1.2124 -0.0000
O 0.7710 1.1685 0.0000
H -1.8198 -0.4847 -0.8141
H -1.8198 -0.4847 0.8141
H -1.5440 1.9671 0.0000
H -2.7722 1.2580 -0.8188
H -2.7722 1.2580 0.8188
H 1.7395 0.9195 0.0000

D 3 2 1 5 S 36 10.0

EOF
36 changes: 36 additions & 0 deletions ...les/gaussian/CT_CT_C_OH/input/starting_coords/protonated_fragment_CT_CT_C_OH_in_COOH.mol2
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@<TRIPOS>MOLECULE
TMP
11 10 1 0 0
SMALL
NO_CHARGES
****
Energy = 0

@<TRIPOS>ATOM
1 C 0.0000 0.0000 0.0000 C 1 TMP 0.000000
2 C -1.5000 0.0000 0.0000 C 1 TMP 0.000000
3 C -2.2000 1.2124 0.0000 C 1 TMP 0.000000
4 O 0.7000 -1.2124 -0.0000 O 1 TMP 0.000000
5 O 0.7710 1.1685 0.0000 O 1 TMP 0.000000
6 H -1.8198 -0.4847 -0.8141 H 1 TMP 0.000000
7 H -1.8198 -0.4847 0.8141 H 1 TMP 0.000000
8 H -1.5440 1.9671 0.0000 H 1 TMP 0.000000
9 H -2.7722 1.2580 -0.8188 H 1 TMP 0.000000
10 H -2.7722 1.2580 0.8188 H 1 TMP 0.000000
11 H 1.7395 0.9195 0.0000 H 1 TMP 0.000000
@<TRIPOS>BOND
1 1 2 1
2 1 4 2
3 1 5 1
4 2 3 1
5 2 6 1
6 2 7 1
7 3 8 1
8 3 9 1
9 3 10 1
10 5 11 1

@<TRIPOS>SUBSTRUCTURE
1 **** 1 TEMP 0 **** **** 0 ROOT

#generated by VMD
36 changes: 36 additions & 0 deletions ..._C_OH/input/starting_coords/protonated_fragment_CT_CT_C_OH_in_COOH_bad_element_order.mol2
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@@ -0,0 +1,36 @@
@<TRIPOS>MOLECULE
TMP
11 10 1 0 0
SMALL
NO_CHARGES
****
Energy = 0

@<TRIPOS>ATOM
1 C 0.0000 0.0000 0.0000 C 1 TMP 0.000000
2 C -1.5000 0.0000 0.0000 C 1 TMP 0.000000
3 O -2.2000 1.2124 0.0000 O 1 TMP 0.000000
4 C 0.7000 -1.2124 -0.0000 C 1 TMP 0.000000
5 O 0.7710 1.1685 0.0000 O 1 TMP 0.000000
6 H -1.8198 -0.4847 -0.8141 H 1 TMP 0.000000
7 H -1.8198 -0.4847 0.8141 H 1 TMP 0.000000
8 H -1.5440 1.9671 0.0000 H 1 TMP 0.000000
9 H -2.7722 1.2580 -0.8188 H 1 TMP 0.000000
10 H -2.7722 1.2580 0.8188 H 1 TMP 0.000000
11 H 1.7395 0.9195 0.0000 H 1 TMP 0.000000
@<TRIPOS>BOND
1 1 2 1
2 1 3 2
3 1 5 1
4 2 4 1
5 2 6 1
6 2 7 1
7 4 8 1
8 4 9 1
9 4 10 1
10 5 11 1

@<TRIPOS>SUBSTRUCTURE
1 **** 1 TEMP 0 **** **** 0 ROOT

#generated by VMD
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