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@chrisjonesBSU
chrisjonesBSU authored Dec 18, 2024
2 parents 3255f30 + 5cfa964 commit 1cd7fc5
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2 changes: 1 addition & 1 deletion environment-dev.yml
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Expand Up @@ -12,7 +12,7 @@ dependencies:
- pydantic>=2
- networkx
- pytest
- mbuild>=0.17.0
- mbuild>=1.1
- openbabel>=3.0.0
- foyer>=0.11.3
- forcefield-utilities>=0.2.1
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6 changes: 4 additions & 2 deletions gmso/tests/base_test.py
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Expand Up @@ -76,15 +76,17 @@ def typed_benzene_ua_system(self, benzene_ua_box):
@pytest.fixture
def benzene_aa(self):
compound = mb.load(get_fn("benzene.mol2"))
compound.children[0].name = "BenzeneAA"
compound.flatten()
compound.name = "BenzeneAA"
top = from_mbuild(compound)
top.identify_connections()
return top

@pytest.fixture
def benzene_aa_box(self):
compound = mb.load(get_fn("benzene.mol2"))
compound.children[0].name = "BenzeneAA"
compound.flatten()
compound.name = "BenzeneAA"
compound_box = mb.packing.fill_box(compound=compound, n_compounds=5, density=1)
top = from_mbuild(compound_box)
top.identify_connections()
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177 changes: 58 additions & 119 deletions gmso/tests/files/charmm.lammps
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@@ -1,130 +1,69 @@
calcraven written by Topology at 2023-12-07 19:10:26.697824 using the GMSO LAMMPS Writer
Using Forcefield Topology_ForceField

9 atoms
8 bonds
12 angles
12 dihedrals
5 impropers

6 atom types
5 bond types
7 angle types
5 dihedral types
3 improper types

0.000000 20.000000 xlo xhi
0.000000 20.000000 ylo yhi
0.000000 20.000000 zlo zhi
0.000000 0.000000 0.000000 xy xz yz
charmm.lammps - created by mBuild; units = real

4 atoms
3 bonds
3 angles
0 dihedrals
1 impropers

4 atom types
3 bond types
3 angle types
1 improper types

0.000000 25.000000 xlo xhi
0.000000 15.000000 ylo yhi
0.000000 6.000000 zlo zhi

Masses
# mass (amu)
1 12.010 # c
2 12.010 # c3
3 19.000 # f
4 1.008 # hn
5 14.010 # n
6 16.000 # o

Pair Coeffs # 4*epsilon*(-sigma**6/r**6 + sigma**12/r**12)
# epsilon (kcal/mol) sigma (Å)
1 0.08600 3.39967 # c
2 0.10940 3.39967 # c3
3 0.06100 3.11815 # f
4 0.01570 1.06908 # hn
5 0.17000 3.25000 # n
6 0.21000 2.95992 # o

Bond Coeffs #LAMMPSHarmonicBondPotential
# k (kcal/(mol*Å**2)) r_eq (Å)
1 313.000000 1.524100 # c c3
2 427.600000 1.378900 # c n
3 637.700000 1.218300 # c o
4 356.900000 1.349700 # c3 f
5 403.200000 1.012900 # hn n

Angle Coeffs #LAMMPSHarmonicAnglePotential
# k (kcal/(mol*rad**2)) theta_eq (degrees)
1 66.800000 115.180000 #c3 c n
2 67.400000 123.200000 #c3 c o
3 74.200000 123.050000 #n c o
4 66.300000 110.000000 #c c3 f
5 70.900000 107.360000 #f c3 f
6 48.300000 117.550000 #c n hn
7 39.600000 117.950000 #hn n hn

Dihedral Coeffs #PeriodicTorsionPotential
# k (kcal/mol) n (dimensionless) phi_eq (degrees) weights (dimensionless)
1 2.500000 2 180 0.0 # n c c3 f
2 1.200000 2 180 0.0 # o c c3 f
3 10.000000 2 180 0.0 # c3 c n hn
4 2.500000 2 180 0.0 # o c n hn
5 2.000000 1 0 0.0 # o c n hn

Improper Coeffs #PeriodicTorsionPotential
# k (kcal/mol) d (dimensionless) phi_eq (degrees)
1 1.100000 2 180
2 1.100000 2 180
3 1.100000 2 180

Atoms #full

1 1 1 0.489360 0.110700 -0.58950 0.021100
2 1 6 -0.40437 -0.03070 -1.83510 -0.10770
3 1 2 0.523890 -0.97100 0.342700 -0.43070
4 1 3 -0.18349 -1.41570 1.088800 0.644700
5 1 3 -0.18349 -2.03550 -0.36720 -0.95820
6 1 3 -0.18349 -0.47200 1.192900 -1.39980
7 1 5 -0.74567 1.308100 -0.07150 0.600200
8 1 4 0.343630 1.442000 0.957800 0.714400
9 1 4 0.343630 2.064000 -0.71890 0.916100

1 12.011000 # CL
2 12.011000 # CTL2
3 15.994000 # OBL
4 15.994000 # OHL

Pair Coeffs # lj
# epsilon (kcal/mol) sigma (Angstrom)
1 0.07000 3.56359 # CL
2 0.05600 3.58141 # CTL2
3 0.12000 3.02906 # OBL
4 0.15210 3.15378 # OHL

Bond Coeffs # harmonic
# k(kcal/mol/angstrom^2) req(angstrom)
1 200.0 1.522 # CL CTL2
2 750.0 1.22 # CL OBL
3 230.0 1.4 # CL OHL

Angle Coeffs # charmm
# k(kcal/mol/rad^2) theteq(deg) k(kcal/mol/angstrom^2) req(angstrom)
1 70.0 125.00000 20.00000 2.44200
2 55.0 110.50000 0.00000 0.00000
3 50.0 123.00000 210.00000 2.26200

Improper Coeffs # harmonic
#k, phi
1 100.00000 0.00000 # CL CTL2 OBL OHL

Atoms # full

1 1 2 0.000000 -10.000000 0.000000 0.000000
2 1 1 0.000000 0.000000 0.000000 0.000000
3 1 3 0.000000 10.000000 0.000000 0.000000
4 1 4 0.000000 0.000000 10.000000 0.000000

Bonds

1 3 1 2
2 1 1 3
3 2 1 7
4 4 3 4
5 4 3 5
6 4 3 6
7 5 7 8
8 5 7 9
1 1 1 2
2 2 2 3
3 3 2 4

Angles

1 2 2 1 3
2 3 2 1 7
3 1 3 1 7
4 4 1 3 4
5 4 1 3 5
6 4 1 3 6
7 5 4 3 5
8 5 4 3 6
9 5 5 3 6
10 6 1 7 8
11 6 1 7 9
12 7 8 7 9

Dihedrals

1 2 2 1 3 4
2 2 2 1 3 5
3 2 2 1 3 6
4 4 2 1 7 8
5 5 2 1 7 8
6 4 2 1 7 9
7 5 2 1 7 9
8 3 3 1 7 8
9 3 3 1 7 9
10 1 7 1 3 4
11 1 7 1 3 5
12 1 7 1 3 6
1 1 1 2 3
2 2 1 2 4
3 3 3 2 4

Impropers

1 1 1 2 3 7
2 2 3 1 4 5
3 2 3 1 4 6
4 2 3 1 5 6
5 3 7 1 8 9
1 1 2 1 3 4
104 changes: 104 additions & 0 deletions gmso/tests/files/parmed-ethane.mcf
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!*******************************************************************************
!Molecular connectivity file
!*******************************************************************************
!parmed-ethane.mcf - created by mBuild

!Atom Format
!index type element mass charge vdw_type parameters
!vdw_type="LJ", parms=epsilon sigma
!vdw_type="Mie", parms=epsilon sigma repulsion_exponent dispersion_exponent

# Atom_Info
8
1 opls_135 C 12.011 -0.18000000 LJ 33.21249 3.50000
2 opls_140 H 1.008 0.06000000 LJ 15.09659 2.50000
3 opls_140 H 1.008 0.06000000 LJ 15.09659 2.50000
4 opls_140 H 1.008 0.06000000 LJ 15.09659 2.50000
5 opls_135 C 12.011 -0.18000000 LJ 33.21249 3.50000
6 opls_140 H 1.008 0.06000000 LJ 15.09659 2.50000
7 opls_140 H 1.008 0.06000000 LJ 15.09659 2.50000
8 opls_140 H 1.008 0.06000000 LJ 15.09659 2.50000

!Bond Format
!index i j type parameters
!type="fixed", parms=bondLength

# Bond_Info
7
1 1 2 fixed 1.090
2 1 3 fixed 1.090
3 1 4 fixed 1.090
4 1 5 fixed 1.529
5 5 6 fixed 1.090
6 5 7 fixed 1.090
7 5 8 fixed 1.090

!Angle Format
!index i j k type parameters
!type="fixed", parms=equilibrium_angle
!type="harmonic", parms=force_constant equilibrium_angle

# Angle_Info
12
1 1 5 6 harmonic 18870.7 110.70
2 1 5 7 harmonic 18870.7 110.70
3 1 5 8 harmonic 18870.7 110.70
4 2 1 3 harmonic 16606.2 107.80
5 2 1 4 harmonic 16606.2 107.80
6 2 1 5 harmonic 18870.7 110.70
7 3 1 4 harmonic 16606.2 107.80
8 3 1 5 harmonic 18870.7 110.70
9 4 1 5 harmonic 18870.7 110.70
10 6 5 7 harmonic 16606.2 107.80
11 6 5 8 harmonic 16606.2 107.80
12 7 5 8 harmonic 16606.2 107.80

!Dihedral Format
!index i j k l type parameters
!type="none"
!type="CHARMM", parms=a0 a1 delta
!type="OPLS", parms=c0 c1 c2 c3
!type="harmonic", parms=force_constant equilibrium_dihedral

# Dihedral_Info
9
1 2 1 5 6 OPLS 0.000 0.000 -0.000 0.628
2 2 1 5 7 OPLS 0.000 0.000 -0.000 0.628
3 2 1 5 8 OPLS 0.000 0.000 -0.000 0.628
4 3 1 5 6 OPLS 0.000 0.000 -0.000 0.628
5 3 1 5 7 OPLS 0.000 0.000 -0.000 0.628
6 3 1 5 8 OPLS 0.000 0.000 -0.000 0.628
7 4 1 5 6 OPLS 0.000 0.000 -0.000 0.628
8 4 1 5 7 OPLS 0.000 0.000 -0.000 0.628
9 4 1 5 8 OPLS 0.000 0.000 -0.000 0.628

!Improper Format
!index i j k l type parameters
!type="harmonic", parms=force_constant equilibrium_improper

# Improper_Info
0

!Fragment Format
!index number_of_atoms_in_fragment branch_point other_atoms

# Fragment_Info
2
1 5 1 2 3 4 5
2 5 5 1 6 7 8


# Fragment_Connectivity
1
1 1 2

!Intra Scaling
!vdw_scaling 1-2 1-3 1-4 1-N
!charge_scaling 1-2 1-3 1-4 1-N

# Intra_Scaling
0. 0. 0.5000 1.
0. 0. 0.5000 1.


END
60 changes: 30 additions & 30 deletions gmso/tests/files/restrained_benzene_ua.gro
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Topology written by GMSO 0.9.1 at 2022-11-07 11:51:34.770776
30
1Compo _CH 1 5.127 3.773 4.686
1Compo _CH 2 5.204 3.757 4.802
1Compo _CH 3 5.343 3.766 4.796
1Compo _CH 4 5.407 3.793 4.674
1Compo _CH 5 5.330 3.809 4.558
1Compo _CH 6 5.191 3.800 4.564
2Compo _CH 7 3.490 3.266 4.318
2Compo _CH 8 3.547 3.139 4.298
2Compo _CH 9 3.552 3.048 4.404
2Compo _CH 10 3.500 3.084 4.530
2Compo _CH 11 3.444 3.210 4.549
2Compo _CH 12 3.439 3.302 4.443
3Compo _CH 13 6.609 1.796 0.837
3Compo _CH 14 6.516 1.728 0.758
3Compo _CH 15 6.535 1.593 0.727
3Compo _CH 16 6.648 1.526 0.776
3Compo _CH 17 6.741 1.594 0.855
3Compo _CH 18 6.721 1.729 0.886
4Compo _CH 19 6.543 2.442 2.196
4Compo _CH 20 6.657 2.484 2.126
4Compo _CH 21 6.644 2.558 2.008
4Compo _CH 22 6.517 2.591 1.960
4Compo _CH 23 6.403 2.549 2.029
4Compo _CH 24 6.416 2.474 2.147
5Compo _CH 25 6.699 5.604 7.130
5Compo _CH 26 6.652 5.661 7.011
5Compo _CH 27 6.611 5.795 7.010
5Compo _CH 28 6.618 5.872 7.127
5Compo _CH 29 6.666 5.814 7.245
5Compo _CH 30 6.706 5.680 7.247
1Benze _CH 1 5.127 3.773 4.686
1Benze _CH 2 5.204 3.757 4.802
1Benze _CH 3 5.343 3.766 4.796
1Benze _CH 4 5.407 3.793 4.674
1Benze _CH 5 5.330 3.809 4.558
1Benze _CH 6 5.191 3.800 4.564
2Benze _CH 7 3.490 3.266 4.318
2Benze _CH 8 3.547 3.139 4.298
2Benze _CH 9 3.552 3.048 4.404
2Benze _CH 10 3.500 3.084 4.530
2Benze _CH 11 3.444 3.210 4.549
2Benze _CH 12 3.439 3.302 4.443
3Benze _CH 13 6.609 1.796 0.837
3Benze _CH 14 6.516 1.728 0.758
3Benze _CH 15 6.535 1.593 0.727
3Benze _CH 16 6.648 1.526 0.776
3Benze _CH 17 6.741 1.594 0.855
3Benze _CH 18 6.721 1.729 0.886
4Benze _CH 19 6.543 2.442 2.196
4Benze _CH 20 6.657 2.484 2.126
4Benze _CH 21 6.644 2.558 2.008
4Benze _CH 22 6.517 2.591 1.960
4Benze _CH 23 6.403 2.549 2.029
4Benze _CH 24 6.416 2.474 2.147
5Benze _CH 25 6.699 5.604 7.130
5Benze _CH 26 6.652 5.661 7.011
5Benze _CH 27 6.611 5.795 7.010
5Benze _CH 28 6.618 5.872 7.127
5Benze _CH 29 6.666 5.814 7.245
5Benze _CH 30 6.706 5.680 7.247
8.42655 8.42655 8.42655
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