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@williamyxl
williamyxl authored Sep 11, 2023
1 parent f9c5a06 commit 1c6f6d3
Showing 1 changed file with 32 additions and 22 deletions.
54 changes: 32 additions & 22 deletions mofa/simulation/raspa.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,19 +88,19 @@ def write_pseudo_atoms_def(
atom_df["element"] = atom_df["type"].map(
dict(zip(mass_df["type"].to_list(), mass_df["comment"].to_list())))
_pseudo_atoms_df = pd.read_csv(
io.StringIO("""He yes He He 0 4.002602 0.0 0.0 1.0 1.0 0 0 relative 0
C_co2 yes C C 0 12.0 0.6512 0.0 1.0 0.720 0 0 relative 0
O_co2 yes O O 0 15.9994 -0.3256 0.0 1.0 0.68 0 0 relative 0
O_o2 yes O O 0 15.9994 -0.112 0.0 1.0 0.7 0 0 relative 0
O_com no O - 0 0.0 0.224 0.0 1.0 0.7 0 0 relative 0
N_n2 yes N N 0 14.00674 -0.405 0.0 1.0 0.7 0 0 relative 0
N_com no N - 0 0.0 0.810 0.0 1.0 0.7 0 0 relative 0
Ar yes Ar Ar 0 39.948 0.0 0.0 1.0 0.7 0 0 relative 0
CH4 yes C C 0 16.04246 0.0 0.0 1.0 1.00 0 0 relative 0
CH3 yes C C 0 15.03452 0.0 0.0 1.0 1.00 0 0 relative 0
CH2 yes C C 0 14.02658 0.0 0.0 1.0 1.00 0 0 relative 0
CH yes C C 0 13.01864 0.0 0.0 1.0 1.00 0 0 relative 0
C yes C C 0 12.0 0.0 0.0 1.0 1.00 0 0 relative 0
io.StringIO("""He yes He He 0 4.002602 0.0 0.0 1.0 1.0 0 0 relative 0
C_co2 yes C C 0 12.0 0.6512 0.0 1.0 0.720 0 0 relative 0
O_co2 yes O O 0 15.9994 -0.3256 0.0 1.0 0.68 0 0 relative 0
O_o2 yes O O 0 15.9994 -0.112 0.0 1.0 0.7 0 0 relative 0
O_com no O - 0 0.0 0.224 0.0 1.0 0.7 0 0 relative 0
N_n2 yes N N 0 14.00674 -0.405 0.0 1.0 0.7 0 0 relative 0
N_com no N - 0 0.0 0.810 0.0 1.0 0.7 0 0 relative 0
Ar yes Ar Ar 0 39.948 0.0 0.0 1.0 0.7 0 0 relative 0
CH4 yes C C 0 16.04246 0.0 0.0 1.0 1.00 0 0 relative 0
CH3 yes C C 0 15.03452 0.0 0.0 1.0 1.00 0 0 relative 0
CH2 yes C C 0 14.02658 0.0 0.0 1.0 1.00 0 0 relative 0
CH yes C C 0 13.01864 0.0 0.0 1.0 1.00 0 0 relative 0
C yes C C 0 12.0 0.0 0.0 1.0 1.00 0 0 relative 0
"""),
sep=r"\s+",
header=None,
Expand All @@ -119,7 +119,8 @@ def write_pseudo_atoms_def(
"anisotropic",
"anisotropic-type",
"tinker-type"])
pseudo_atoms_df_header_str = "#type print as chem oxidation mass charge polarization B-factor radii connectivity anisotropic anisotropic-type tinker-type"
pseudo_atoms_df_header_str = "#type print as chem oxidation mass" + " " + \
"charge polarization B-factor radii connectivity anisotropic anisotropic-type tinker-type"
pseudo_atoms_df = atom_df[["comment", "element", "element", "mass", "q"]].copy(
deep=True).reset_index(drop=True)
pseudo_atoms_df.columns = ["#type", "as", "chem", "mass", "charge"]
Expand Down Expand Up @@ -178,7 +179,8 @@ def write_force_field_mixing_rules_def(
kCal2Joule = 4184
lammps2raspa_energy = kCal2Joule / (NAvogadro * kB)
_mixing_df = read_lmp_sec_str2df(
"""He lennard-jones 10.9 2.64 // J.O. Hirschfelder et al., Molecular Theory of Gases and Liquids, Wiley, New York, 1954, p. 1114.
"""He lennard-jones 10.9 2.64""" +
" " + """// J.O. Hirschfelder et al., Molecular Theory of Gases and Liquids, Wiley, New York, 1954, p. 1114.
O_co2 lennard-jones 85.671 3.017 // A. Garcia-Sanchez et al., J. Phys. Chem. C 2009, 113, 8814-8820.
C_co2 lennard-jones 29.933 2.745 // idem
N_n2 lennard-jones 38.298 3.306 // A. Martin-Calvo et al. , Phys. Chem. Chem. Phys. 2011, 13, 11165-11174.
Expand Down Expand Up @@ -424,7 +426,9 @@ def write_framework_def(self, raspa_path: str,

header_df = pd.read_csv(
io.StringIO(
"""#CoreShells bond BondDipoles UreyBradley bend inv tors improper-torsion bond/bond bond/bend bend/bend stretch/torsion bend/torsion
"""#CoreShells bond BondDipoles UreyBradley bend inv tors""" +
" " +
"""improper-torsion bond/bond bond/bend bend/bend stretch/torsion bend/torsion
0 """ +
"%d" %
len(bond_df) +
Expand Down Expand Up @@ -749,8 +753,10 @@ def prep_raspa_single(
1
# atomic positions
0 He
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion""" + " " + \
"""Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 0 0 0 0 0 0 0""" + " " + \
"""0 0 0 0 0 0 0
# Number of config moves
0
"""
Expand Down Expand Up @@ -846,8 +852,10 @@ def prep_raspa_single(
0 O_co2 0.0 0.0 1.149
1 C_co2 0.0 0.0 0.0
2 O_co2 0.0 0.0 -1.149
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 2 0 0 0 0 0 0 0 0 0 0 0 0 0
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond""" + " " + \
"""Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 2 0 0 0 0 0 0 0""" + " " + \
"""0 0 0 0 0 0
# Bond stretch: atom n1-n2, type, parameters
0 1 RIGID_BOND
1 2 RIGID_BOND
Expand Down Expand Up @@ -966,8 +974,10 @@ def prep_raspa_single(
0 O_co2 0.0 0.0 1.149
1 C_co2 0.0 0.0 0.0
2 O_co2 0.0 0.0 -1.149
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 2 0 0 0 0 0 0 0 0 0 0 0 0 0
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond""" + " " + \
"""Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 2 0 0 0 0 0 0 0""" + " " + \
"""0 0 0 0 0 0
# Bond stretch: atom n1-n2, type, parameters
0 1 RIGID_BOND
1 2 RIGID_BOND
Expand Down

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