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lammps.py
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lammps.py
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# -*- coding: utf-8 -*-
"""A node or step for LAMMPS in a flowchart"""
import copy
import glob
import logging
from math import sqrt, exp, degrees, radians, cos, acos
from pathlib import Path
import os
import os.path
import pkg_resources
import pprint
import re
import shutil
import string
import sys
import traceback
import bibtexparser
import numpy
import pandas
import psutil
from scipy.stats import t as t_student
import statsmodels.tsa.stattools as stattools
import lammps_step
import molsystem
import seamm
import seamm_util
import seamm_util.printing as printing
from seamm_util.printing import FormattedText as __
from pymbar import timeseries
logger = logging.getLogger("lammps")
job = printing.getPrinter()
printer = printing.getPrinter("lammps")
# Add LAMMPS's properties to the standard properties
path = Path(pkg_resources.resource_filename(__name__, "data/"))
csv_file = path / "properties.csv"
molsystem.add_properties_from_file(csv_file)
bond_style = {
"quadratic_bond": "harmonic",
"quartic_bond": "class2",
"fene": "fene",
"morse": "morse",
}
angle_style = {
"quadratic_angle": "harmonic",
"quartic_angle": "class2",
"simple_fourier_angle": "fourier/simple",
}
dihedral_style = {
"torsion_1": "harmonic",
"torsion_3": "class2",
"torsion_opls": "opls",
}
improper_style = {
"wilson_out_of_plane": "class2",
"improper_opls": "cvff",
}
class LAMMPS(seamm.Node):
display_units = {
"T": "K",
"P": "atm",
"t": "fs",
"density": "g/mL",
"a": "Å",
"b": "Å",
"c": "Å",
"Etot": "kcal/mol",
"Eke": "kcal/mol",
"Epe": "kcal/mol",
"Emol": "kcal/mol",
"Epair": "kcal/mol",
}
display_title = {
"T": "Temperature",
"P": "Pressure",
"t": "Time",
"density": "Density",
"a": "a lattice parameter",
"b": "b lattice parameter",
"c": "c lattice parameter",
"Etot": "Total Energy",
"Eke": "Kinetic Energy",
"Epe": "Potential Energy",
"Emol": "Molecular Energy, Valence Terms",
"Epair": "Pair (Nonbond) Energy",
}
def __init__(
self, flowchart=None, namespace="org.molssi.seamm.lammps", extension=None
):
"""Setup the main LAMMPS step
Keyword arguments:
"""
logger.debug("Creating LAMMPS {}".format(self))
# The subflowchart
self.subflowchart = seamm.Flowchart(
parent=self, name="LAMMPS", namespace=namespace
)
self._initialization_node = None
self._trajectory = []
self._data = {}
super().__init__(
flowchart=flowchart, title="LAMMPS", extension=extension, logger=logger
)
@property
def version(self):
"""The semantic version of this module."""
return lammps_step.__version__
@property
def git_revision(self):
"""The git version of this module."""
return lammps_step.__git_revision__
@staticmethod
def box_to_cell(lx, ly, lz, xy, xz, yz):
"""Convert the LAMMPS box definition to cell parameters."""
if xy == 0 and xz == 0 and yz == 0:
a = lx
b = ly
c = lz
alpha = 0.0
beta = 0.0
gamma = 0.0
else:
a = lx
b = sqrt(ly**2 + xy**2)
c = sqrt(lz**2 + xz**2 + yz**2)
alpha = degrees(acos((xy * xz + lx * yz) / (b * c)))
beta = degrees(acos(xz / c))
gamma = degrees(acos(xy / b))
return (a, b, c, alpha, beta, gamma)
@staticmethod
def cell_to_box(a, b, c, alpha, beta, gamma):
"""Convert cell parameters to the LAMMPS box."""
if alpha == 90 and beta == 90 and gamma == 90:
lx = a
ly = b
lz = c
xy = xz = yz = 0.0
else:
lx = 0
xy = b * cos(radians(gamma))
xz = c * cos(radians(beta))
ly = sqrt(b**2 - xy**2)
yz = (b * c * cos(radians(alpha)) - xy * xz) / ly
lz = sqrt(c**2 - xz**2 - yz**2)
return (lx, ly, lz, xy, xz, yz)
def create_parser(self):
"""Setup the command-line / config file parser"""
parser_name = self.step_type
parser = seamm_util.getParser()
# Remember if the parser exists ... this type of step may have been
# found before
parser_exists = parser.exists(parser_name)
# Create the standard options, e.g. log-level
result = super().create_parser(name=parser_name)
if parser_exists:
return result
# LAMMPS specific options
parser.add_argument(
parser_name,
"--ncores",
default="available",
help=(
"The maximum number of cores to use for LAMMPS. "
"Default: all available cores."
),
)
parser.add_argument(
parser_name,
"--atoms-per-core",
type=int,
default="1000",
help="the optimal number of atoms per core for LAMMPS",
)
parser.add_argument(
parser_name,
"--html",
action="store_true",
help="whether to write out html files for graphs, etc.",
)
parser.add_argument(
parser_name,
"--modules",
nargs="*",
default=None,
help="the environment modules to load for LAMMPS",
)
parser.add_argument(
parser_name,
"--lammps-path",
default=None,
help="the path to the LAMMPS executables",
)
parser.add_argument(
parser_name,
"--lammps-serial",
default="lmp_serial",
help="the serial version of LAMMPS",
)
parser.add_argument(
parser_name,
"--lammps-mpi",
default="lmp_mpi",
help="the mpi version of LAMMPS",
)
parser.add_argument(
parser_name, "--mpiexec", default="mpiexec", help="the mpi executable"
)
return result
def set_id(self, node_id):
"""Set the id for node to a given tuple"""
self._id = node_id
# and set our subnodes
self.subflowchart.set_ids(self._id)
return self.next()
def description_text(self, P=None):
"""Return a short description of this step.
Return a nicely formatted string describing what this step will
do.
Keyword arguments:
P: a dictionary of parameter values, which may be variables
or final values. If None, then the parameters values will
be used as is.
"""
self.subflowchart.root_directory = self.flowchart.root_directory
# Get the first real node
node = self.subflowchart.get_node("1").next()
text = self.header + "\n\n"
while node is not None:
try:
text += __(node.description_text(), indent=3 * " ").__str__()
except Exception as e:
print(
"Error describing LAMMPS flowchart: {} in {}".format(
str(e), str(node)
)
)
self.logger.critical(
"Error describing LAMMPS flowchart: {} in {}".format(
str(e), str(node)
)
)
raise
except: # noqa: E722
print(
"Unexpected error describing LAMMPS flowchart: {} in {}".format(
sys.exc_info()[0], str(node)
)
)
self.logger.critical(
"Unexpected error describing LAMMPS flowchart: {} in {}".format(
sys.exc_info()[0], str(node)
)
)
raise
text += "\n"
node = node.next()
return text
def run(self):
"""Run a LAMMPS simulation"""
system_db = self.get_variable("_system_db")
configuration = system_db.system.configuration
n_atoms = configuration.n_atoms
if n_atoms == 0:
self.logger.error("LAMMPS run(): there is no structure!")
raise RuntimeError("LAMMPS run(): there is no structure!")
next_node = super().run(printer)
# Get the options
o = self.options
global_options = self.global_options
# Whether to run parallel and if so, how many mpi processes
if global_options["parallelism"] in ("any", "mpi"):
np = o["ncores"]
if np == "available":
np = global_options["ncores"]
if np == "available":
np = int(round(n_atoms / o["atoms_per_core"]))
if np < 1:
np = 1
# How many processors does this node have?
n_cores = psutil.cpu_count(logical=False)
self.logger.info("The number of cores is {}".format(n_cores))
if np > n_cores:
self.logger.info(
f"LAMMPS could use {np} cores, but only {n_cores} are "
"available"
)
np = n_cores
else:
np = int(np)
else:
np = 1
# Print headers and get to work
printer.important(self.header)
if np > 1:
printer.important(" LAMMPS using MPI with {} processes.\n".format(np))
else:
printer.important(" LAMMPS using the serial version.\n")
self.subflowchart.root_directory = self.flowchart.root_directory
files = {}
# Get the first real node
node = self.subflowchart.get_node("1").next()
extras = {}
history_nodes = []
# Create overall directory for the lammps step
os.makedirs(self.directory, exist_ok=True)
files = {}
while node is not None:
if isinstance(node, lammps_step.Initialization):
initialization_header, eex = self._get_node_input(
node=node, extras={"read_data": True}
)
files["structure"] = {}
files["structure"]["filename"] = "structure.dat"
files["structure"]["data"] = "\n".join(self.structure_data(eex))
f = os.path.join(self.directory, files["structure"]["filename"])
with open(f, mode="w") as fd:
fd.write(files["structure"]["data"])
self.logger.debug(
files["structure"]["filename"] + ": " + files["structure"]["data"]
)
self._initialization_node = node
files["input"] = {}
files["input"]["filename"] = None
files["input"]["data"] = copy.deepcopy(initialization_header)
# Find the bond & angle types as needed for shake/rattle
P = node.parameters.current_values_to_dict(
context=seamm.flowchart_variables._data
)
shake = self.shake_fix(P, eex)
if shake != "":
extras["shake"] = shake
else:
P = node.parameters.current_values_to_dict(
context=seamm.flowchart_variables._data
)
if "run_control" not in P or "Until" not in P["run_control"]:
history_nodes.append(node)
else:
if len(history_nodes) > 0: # if imcccc
files = self._prepare_input(
files,
nodes=history_nodes,
read_restart=False,
write_restart=True,
extras=extras,
)
files = self._execute_single_sim(files, np=np)
self.analyze(nodes=history_nodes)
self._trajectory = []
iteration = 0
extras["nsteps"] = 666
while True:
extras["nsteps"] = round(1.5 * extras["nsteps"])
control_properties = {}
for prp in P["control_properties"]:
k = prp[0]
control_properties[k] = {
"accuracy": float(prp[1][0].strip("%")),
"units": prp[1][1],
"enough_accuracy": False,
}
P = node.parameters.current_values_to_dict(
context=seamm.flowchart_variables._data
)
files = self._prepare_input(
files,
nodes=node,
iteration=iteration,
read_restart=True,
write_restart=True,
extras=extras,
)
files = self._execute_single_sim(files, np=np)
# Analyze the results
analysis = self.analyze(nodes=node)
node_id = node._id[1]
for prp, v in analysis[node_id].items():
if v["short_production"] is False:
if v["few_neff"] is False:
accuracy = control_properties[prp]["accuracy"] / 100
dof = v["n_sample"]
mean = v["mean"]
ci = t_student.interval(
0.95, dof - 1, loc=0, scale=1
)
interval = (ci[1] - ci[0]) * v["sem"]
print(abs(interval / mean))
if abs(interval / mean) < accuracy:
control_properties[prp][
"enough_accuracy"
] = True
enough_acc = [
v["enough_accuracy"]
for prp, v in control_properties.items()
]
if all(enough_acc) is True:
history_nodes = []
initialization_header, eex = self._get_node_input(
node=self._initialization_node,
extras={"read_data": False},
)
files["input"]["data"] = copy.deepcopy(
initialization_header
)
files["input"]["data"].append(
"read_restart %s"
% (os.path.join(files["restart"]["filename"]))
)
self._trajectory = []
break
iteration = iteration + 1
node = node.next()
if len(history_nodes) == 0:
node_initialization = self.subflowchart.get_node("1").next()
if node_initialization is None:
raise TypeError(
"The initial node in a LAMMPS workflow should be an ",
"initialization node",
)
if isinstance(node_initialization, lammps_step.Initialization) is False:
raise TypeError(
"The initial node in a LAMMPS workflow should be an ",
"initialization node",
)
# base = "lammps_substep_%s_iter_%d" % (node_initialization._id[1], 0)
base = "lammps"
restart = base + ".restart.*"
dump = base + ".dump.*"
input_file = base + ".dat"
new_input_data = []
new_input_data.append("run 0")
new_input_data.append(f"write_restart {restart}")
new_input_data.append(
f"write_dump all custom {dump} id " "xu yu zu modify flush yes sort id"
)
files["input"]["filename"] = input_file
files["input"]["data"] += new_input_data
files["input"]["data"] = "\n".join(files["input"]["data"])
self.logger.debug(
files["input"]["filename"] + ":\n" + files["input"]["data"]
)
files = self._execute_single_sim(files, np=np)
if len(history_nodes) > 0:
files = self._prepare_input(
files,
nodes=history_nodes,
read_restart=False,
write_restart=True,
extras=extras,
)
files = self._execute_single_sim(files, np=np)
self.analyze(nodes=history_nodes)
self._trajectory = []
self.read_dump(os.path.join(self.directory, files["dump"]["filename"]))
printer.normal("")
return next_node
def _execute_single_sim(self, files, np=1, return_files=None):
"""
Step #1: Dump input file
Step #2: Execute input file
Step #3: Dump stderr
Step #4: Dump output files
"""
tmpdict = {}
for k, v in files.items():
if v["filename"] is None or v["data"] is None:
continue
filename = os.path.join(self.directory, v["filename"])
mode = "w" if type(v["data"]) is str else "wb"
with open(filename, mode=mode) as fd:
fd.write(v["data"])
tmpdict[v["filename"]] = v["data"]
return_files = [
"summary_*.txt",
"trajectory_*.seamm_trj",
"*.restart.*",
"*.dump.*",
"*.log",
"*.dat",
"log.cite",
] # yapf: disable
local = seamm.ExecLocal()
# Find the executables and if they exist.
lammps_path = Path(self.options["lammps_path"]).expanduser().resolve()
lmp_serial = lammps_path / self.options["lammps_serial"]
lmp_serial = lmp_serial.expanduser().resolve()
if not lmp_serial.exists():
lmp_serial = None
lmp_mpi = lammps_path / self.options["lammps_mpi"]
lmp_mpi = lmp_mpi.expanduser().resolve()
if lmp_mpi.exists():
mpiexec = lammps_path / self.options["mpiexec"]
mpiexec = mpiexec.expanduser().resolve()
if not mpiexec.exists():
# See if it is in the path
mpiexec = shutil.which(self.options["mpiexec"])
if mpiexec is None:
lmp_mpi = None
else:
mpiexec = Path(mpiexec).expanduser().resolve()
else:
lmp_mpi = None
# Use the parallel executable if the serial does not exist, and vice
# versa
if lmp_mpi is not None and (np > 1 or lmp_serial is None):
cmd = [str(mpiexec), "-np", str(np), str(lmp_mpi)]
else:
cmd = [str(lmp_serial)]
cmd.extend(["-in", files["input"]["filename"]])
result = local.run(
cmd=cmd,
files=tmpdict,
return_files=return_files,
in_situ=True,
directory=self.directory,
)
if result is None:
self.logger.error("There was an error running LAMMPS")
return None
self.logger.debug("\n" + pprint.pformat(result))
self.logger.debug("stdout:\n" + result["stdout"])
f = os.path.join(self.directory, "stdout.txt")
with open(f, mode="w") as fd:
fd.write(result["stdout"])
# Add the citations, getting the version from stdout and any citations
if "log.cite" in result:
self._add_lammps_citations(
result["stdout"], cite=result["log.cite"]["data"]
)
else:
self._add_lammps_citations(result["stdout"])
if result["stderr"] != "":
self.logger.warning("stderr:\n" + result["stderr"])
f = os.path.join(self.directory, "stderr.txt")
with open(f, mode="w") as fd:
fd.write(result["stderr"])
for filename in result["files"]:
f = os.path.join(self.directory, filename)
mode = "wb" if type(result[filename]["data"]) is bytes else "w"
with open(f, mode=mode) as fd:
if result[filename]["data"] is not None:
fd.write(result[filename]["data"])
else:
fd.write(result[filename]["exception"])
base = os.path.basename(files["input"]["filename"][0:-4])
restart_file = base + ".restart.*"
dump_file = base + ".dump.*"
filename = os.path.join(self.directory, restart_file)
restart_filenames = glob.glob(filename)
# Probably the step didn't run
if len(restart_filenames) == 0:
raise FileNotFoundError(
"Lammps_step: could not find any file with the pattern %s" % (filename)
)
run_lengths = []
for f in restart_filenames:
try:
pre, ext = os.path.splitext(f)
ext = int(ext.strip("."))
except ValueError:
raise Exception("Lammps_step: could not extract run length from %s" % f)
run_lengths.append(ext)
last_snapshot = str(max(run_lengths))
restart_file = restart_file.replace("*", last_snapshot)
dump_file = dump_file.replace("*", last_snapshot)
files["restart"] = {}
files["restart"]["filename"] = restart_file
files["dump"] = {}
files["dump"]["filename"] = dump_file
files["dump"]["data"] = None
filename = os.path.join(self.directory, restart_file)
with open(filename, mode="rb") as fd:
files["restart"]["data"] = fd.read()
files["input"] = {}
files["input"]["filename"] = None
initialization_header, eex = self._get_node_input(
node=self._initialization_node, extras={"read_data": False}
)
files["input"]["data"] = copy.deepcopy(initialization_header)
return files
def _prepare_input(
self,
files,
nodes=None,
iteration=0,
read_restart=False,
write_restart=False,
extras=None,
):
if isinstance(nodes, list) is False:
node_ids = [nodes._id[1]]
new_input_data = self._get_node_input(node=nodes, extras=extras)
else:
node_ids = []
new_input_data = []
for n in nodes:
node_ids.append(n._id[1])
new_input_data += self._get_node_input(node=n, extras=extras)
# base = "lammps_substep_%s_iter_%d" % ("_".join(node_ids), iteration)
base = "lammps"
input_file = base + ".dat"
restart = base + ".restart.*"
dump = base + ".dump.*"
if read_restart:
new_input_data.insert(
0, "read_restart %s" % (files["restart"]["filename"])
)
if write_restart:
new_input_data.append(f"write_restart {restart}")
new_input_data.append(
f"write_dump all custom {dump} id " "xu yu zu modify flush yes sort id"
)
files["input"]["data"] += new_input_data
files["input"]["filename"] = input_file
files["input"]["data"] = "\n".join(files["input"]["data"])
self.logger.debug(files["input"]["filename"] + ":\n" + files["input"]["data"])
return files
def _get_node_input(self, node=None, extras=None):
try:
ret = node.get_input(extras=extras)
except Exception as e:
print("Error running LAMMPS flowchart: {} in {}".format(str(e), str(node)))
self.logger.critical(
"Error running LAMMPS flowchart: {} in {}".format(str(e), str(node))
)
raise
except: # noqa: E722
print(
"Unexpected error running LAMMPS flowchart: {} in {}".format(
sys.exc_info()[0], str(node)
)
)
self.logger.critical(
"Unexpected error running LAMMPS flowchart: {} in {}".format(
sys.exc_info()[0], str(node)
)
)
raise
return ret
def structure_data(self, eex, triclinic=False):
"""Create the LAMMPS structure file from the energy expression"""
lines = []
# The terms in the forcefield, and for each a list of forms
terms = eex["terms"]
lines.append("Structure file for LAMMPS generated by a MolSSI flowchart")
lines.append("{:10d} atoms".format(eex["n_atoms"]))
lines.append("{:10d} atom types".format(eex["n_atom_types"]))
if "n_bonds" in eex and eex["n_bonds"] > 0:
lines.append("{:10d} bonds".format(eex["n_bonds"]))
lines.append("{:10d} bond types".format(eex["n_bond_types"]))
if "n_angles" in eex and eex["n_angles"] > 0:
lines.append("{:10d} angles".format(eex["n_angles"]))
lines.append("{:10d} angle types".format(eex["n_angle_types"]))
if "n_torsions" in eex and eex["n_torsions"] > 0:
lines.append("{:10d} dihedrals".format(eex["n_torsions"]))
lines.append("{:10d} dihedral types".format(eex["n_torsion_types"]))
if "n_oops" in eex and eex["n_oops"] > 0:
lines.append("{:10d} impropers".format(eex["n_oops"]))
lines.append("{:10d} improper types".format(eex["n_oop_types"]))
# Find the box limits
periodicity = eex["periodicity"]
if periodicity == 3:
a, b, c, alpha, beta, gamma = eex["cell"]
lx, ly, lz, xy, xz, yz = LAMMPS.cell_to_box(a, b, c, alpha, beta, gamma)
lines.append("{} {} xlo xhi".format(0.0, lx))
lines.append("{} {} ylo yhi".format(0.0, ly))
lines.append("{} {} zlo zhi".format(0.0, lz))
xy = xy if abs(xy) > 1.0e-06 else 0.0
xz = xz if abs(xy) > 1.0e-06 else 0.0
yz = yz if abs(xy) > 1.0e-06 else 0.0
if triclinic or xy > 0.0 or xz > 0.0 or yz > 0.0:
lines.append("{} {} {} xy xz yz".format(xy, xz, yz))
else:
x, y, z, index = eex["atoms"][0]
xlo = xhi = x
ylo = yhi = y
zlo = zhi = z
for x, y, z, index in eex["atoms"]:
xlo = x if x < xlo else xlo
xhi = x if x > xhi else xhi
ylo = y if y < ylo else ylo
yhi = y if y > yhi else yhi
zlo = z if z < zlo else zlo
zhi = z if z > zhi else zhi
# Some extra space....
xlo -= 10.0
xhi += 10.0
ylo -= 10.0
yhi += 10.0
zlo -= 10.0
zhi += 10.0
lines.append("{} {} xlo xhi".format(xlo, xhi))
lines.append("{} {} ylo yhi".format(ylo, yhi))
lines.append("{} {} zlo zhi".format(zlo, zhi))
# the atoms and their masses, etc.
lines.append("")
lines.append("Atoms")
lines.append("")
if "charges" in eex:
if "molecule" in eex:
for i, mol, xyz_index, q in zip(
range(1, eex["n_atoms"] + 1),
eex["molecule"],
eex["atoms"],
eex["charges"],
):
x, y, z, index = xyz_index
lines.append(
f"{i:6d} {mol + 1:6d} {index:6d} {q:6.3f} {x:12.7f} {y:12.7f} "
f"{z:12.7f}"
)
else:
for i, xyz_index, q in zip(
range(1, eex["n_atoms"] + 1), eex["atoms"], eex["charges"]
):
x, y, z, index = xyz_index
lines.append(
f"{i:6d} {index:6d} {q:6.3f} {x:12.7f} {y:12.7f} {z:12.7f}"
)
else:
for i, xyz_index in enumerate(eex["atoms"]):
x, y, z, index = xyz_index
lines.append(f"{i+1:6d} {index:6d} {x:12.7f} {y:12.7f} {z:12.7f}")
lines.append("")
lines.append("Masses")
lines.append("")
self._data["masses"] = []
for i, parameters in zip(range(1, eex["n_atom_types"] + 1), eex["masses"]):
mass, itype = parameters
lines.append("{:6d} {} # {}".format(i, mass, itype))
self._data["masses"].append(float(mass))
# nonbonds
if "nonbond parameters" in eex:
lines.append("")
lines.append("Pair Coeffs")
lines.append("")
for i, parameters in zip(
range(1, eex["n_atom_types"] + 1), eex["nonbond parameters"]
):
form, values, types, parameters_type, real_types = parameters
if form == "nonbond(9-6)":
lines.append(
"{:6d} {} {} # {} --> {}".format(
i, values["eps"], values["rmin"], types[0], real_types[0]
)
)
else:
lines.append(
"{:6d} {} {} # {} --> {}".format(
i, values["eps"], values["sigma"], types[0], real_types[0]
)
)
# bonds
if "n_bonds" in eex and eex["n_bonds"] > 0:
lines.append("")
lines.append("Bonds")
lines.append("")
for counter, tmp in zip(range(1, eex["n_bonds"] + 1), eex["bonds"]):
i, j, index = tmp
lines.append("{:6d} {:6d} {:6d} {:6d}".format(counter, index, i, j))
lines.append("")
lines.append("Bond Coeffs")
lines.append("")
use_hybrid = len(terms["bond"]) > 1
for counter, parameters in zip(
range(1, eex["n_bond_types"] + 1), eex["bond parameters"]
):
form, values, types, parameters_type, real_types = parameters
if form == "quadratic_bond":
function = "harmonic" if use_hybrid else ""
line = f"{counter:6d} {function} " f"{values['K2']} {values['R0']}"
elif form == "quartic_bond":
function = "class2" if use_hybrid else ""
line = (
f"{counter:6d} {function} {values['R0']} "
f"{values['K2']} {values['K3']} {values['K4']}"
)
line += (
f" # {types[0]}-{types[1]}" f" --> {real_types[0]}_{real_types[1]}"
)
lines.append(line)
# angles
if "n_angles" in eex and eex["n_angles"] > 0:
lines.append("")
lines.append("Angles")
lines.append("")
for counter, tmp in zip(range(1, eex["n_angles"] + 1), eex["angles"]):
i, j, k, index = tmp
lines.append(
"{:6d} {:6d} {:6d} {:6d} {:6d}".format(counter, index, i, j, k)
)
lines.append("")
lines.append("Angle Coeffs")
lines.append("")
use_hybrid = len(terms["angle"]) > 1
quartic_function = "class2" if "n_bond-bond_types" in eex else "quartic"
for counter, parameters in zip(
range(1, eex["n_angle_types"] + 1), eex["angle parameters"]
):
form, values, types, parameters_type, real_types = parameters
if form == "quadratic_angle":
function = "harmonic" if use_hybrid else ""
line = (
f"{counter:6d} {function} " f"{values['K2']} {values['Theta0']}"
)
elif form == "quartic_angle":
function = quartic_function if use_hybrid else ""
line = (
f"{counter:6d} {function} {values['Theta0']} "
f"{values['K2']} {values['K3']} {values['K4']}"
)
elif form == "simple_fourier_angle":
function = "fourier/simple" if use_hybrid else ""
line = f"{counter:6d} {function} {values['K']} -1 {values['n']}"
line += (
f" # {types[0]} {types[1]} {types[2]}"
f" --> {real_types[0]} {real_types[1]} {real_types[2]}"
)
lines.append(line)
# bond-bond coefficients, which must match angles in order & number
if "n_bond-bond_types" in eex:
lines.append("")
lines.append("BondBond Coeffs")
lines.append("")
for counter, parameters, angles in zip(
range(1, eex["n_bond-bond_types"] + 1),
eex["bond-bond parameters"],
eex["angle parameters"],
):
form, values, types, parameters_type, real_types = parameters
angle_form = angles[0]
if angle_form == "quartic_angle":
lines.append(
"{:6d} class2 {} {} {}".format(
counter, values["K"], values["R10"], values["R20"]
)
+ " # {}-{}-{} --> {}-{}-{}".format(
types[0],
types[1],
types[2],
real_types[0],
real_types[1],
real_types[2],
)
)
else:
lines.append(
"{:6d} skip".format(counter)
+ " # {}-{}-{} --> {}-{}-{}".format(
types[0],
types[1],
types[2],
real_types[0],