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added logging to Lammps extension
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Ellen Zhong committed Jun 20, 2014
1 parent ba248ce commit 62054dd
Showing 1 changed file with 24 additions and 45 deletions.
69 changes: 24 additions & 45 deletions intermol/lammps_extension/lammps_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,8 @@
.. moduleauthor:: Christoph Klein <[email protected]>
"""
import os
from warnings import warn
import pdb

import logging
import numpy as np

import intermol.unit as units
Expand All @@ -16,6 +15,7 @@
from intermol.Types import *
from intermol.Force import *

logger = logging.getLogger('InterMolLog')

class LammpsParser(object):
"""A class containing methods to read and write LAMMPS files."""
Expand Down Expand Up @@ -146,7 +146,7 @@ def parse_atom_style(self, line):
"""
self.atom_style = line[1]
if len(line) > 2:
warn("Unsupported atom_style in input file.")
logger.warn("Unsupported atom_style in input file.")

def parse_dimension(self, line):
""" """
Expand All @@ -166,7 +166,7 @@ def parse_pair_style(self, line):
""" """
self.pair_style = []
if line[1] == 'hybrid':
warn("Hybrid pair styles not yet implemented.")
logger.warn("Hybrid pair styles not yet implemented.")
elif line[1] == 'lj/cut/coul/long':
self.pair_style.append(line[1])
System._sys._nbFunc = 1
Expand All @@ -188,9 +188,9 @@ def parse_pair_modify(self, line):
elif line[2] == 'arithmetic':
System._sys._combinationRule = 2
else:
warn("Unsupported pair_modify mix argument in input file!")
logger.warn("Unsupported pair_modify mix argument in input file!")
else:
warn("Unsupported pair_modify style in input file!")
logger.warn("Unsupported pair_modify style in input file!")

def parse_bond_style(self, line):
""" """
Expand Down Expand Up @@ -254,14 +254,14 @@ def parse_special_bonds(self, line):
elif 'coul' in line:
System._sys._coulombCorrection = float(line[line.index('coul') + 3])
else:
warn("Unsupported special_bonds in input file.")
logger.warn("Unsupported special_bonds in input file.")

def parse_read_data(self, line):
""" """
if len(line) == 2:
self.data_file = os.path.join(self.basepath, line[1])
else:
warn("Unsupported read_data arguments in input file.")
logger.warn("Unsupported read_data arguments in input file.")

def parse_box(self, line, dim):
"""Read box information from data file.
Expand Down Expand Up @@ -302,9 +302,9 @@ def parse_pair_coeffs(self, data_lines):
self.nb_types[int(fields[0])] = [fields[1] * self.ENERGY,
fields[2] * self.DIST]
else:
warn("Unsupported pair coeff formatting in data file!")
logger.warn("Unsupported pair coeff formatting in data file!")
else:
warn("Unsupported pair coeff formatting in data file!")
logger.warn("Unsupported pair coeff formatting in data file!")

def parse_bond_coeffs(self, data_lines):
"""Read bond coefficients from data file."""
Expand Down Expand Up @@ -444,7 +444,7 @@ def parse_atoms(self, data_lines):
pass
new_atom_type = None
if System._sys._combinationRule == 1:
warn("Combination rule '1' not yet implemented")
logger.warn("Combination rule '1' not yet implemented")
elif System._sys._combinationRule in [2, 3]:
new_atom_type = AtomCR23Type(fields[2], # atomtype
fields[2], # bondtype
Expand Down Expand Up @@ -478,7 +478,7 @@ def parse_atoms(self, data_lines):
atom.setEpsilon(ab_state, atom_type.epsilon)
atom.bondtype = atom_type.bondtype
else:
warn("Corresponding AtomType was not found. "
logger.warn("Corresponding AtomType was not found. "
"Insert missing values yourself.")
self.current_mol.addAtom(atom)

Expand Down Expand Up @@ -669,10 +669,7 @@ def write(self, data_file, unit_set='real', verbose=False):

# read all atom specific and FF information
for mol_type in System._sys._molecules.itervalues():
if verbose:
import time
mol_start = time.time()
print " Writing moleculetype {0}...".format(mol_type.name)
logger.debug(" Writing moleculetype {0}...".format(mol_type.name))
# atom index offsets from 1 for each molecule
offsets = list()
for molecule in mol_type.moleculeSet:
Expand All @@ -681,9 +678,7 @@ def write(self, data_file, unit_set='real', verbose=False):
molecule = mol_type.moleculeSet[0]
atoms = molecule._atoms
for i, offset in enumerate(offsets):
if verbose:
start = time.time()
print " Writing bonds..."
logger.debug(" Writing bonds...")
for j, bond in enumerate(mol_type.bondForceSet.itervalues()):
atomtype1 = molecule._atoms[bond.atom1 - 1].bondtype
atomtype2 = molecule._atoms[bond.atom2 - 1].bondtype
Expand Down Expand Up @@ -715,7 +710,7 @@ def write(self, data_file, unit_set='real', verbose=False):
bond.length.in_units_of(self.DIST)._value))
b_type_i += 1
else:
warn("Found unimplemented bond type for LAMMPS!")
logger.warn("Found unimplemented bond type for LAMMPS!")
continue

bond_list.append('{0:-6d} {1:6d} {2:6d} {3:6d}\n'.format(
Expand All @@ -725,14 +720,10 @@ def write(self, data_file, unit_set='real', verbose=False):
bond.atom2 + offset))
bond_style.add(style)
if len(bond_style) > 1:
warn("More than one bond style found!")
if verbose:
print " Done. ({0:.2f} s)".format(time.time() - start)
logger.warn("More than one bond style found!")

# angle types
if verbose:
start = time.time()
print " Writing angles..."
logger.debug(" Writing angles...")
for j, angle in enumerate(mol_type.angleForceSet.itervalues()):
atomtype1 = molecule._atoms[angle.atom1 - 1].bondtype
atomtype2 = molecule._atoms[angle.atom2 - 1].bondtype
Expand Down Expand Up @@ -780,7 +771,7 @@ def write(self, data_file, unit_set='real', verbose=False):
angle.theta.in_units_of(self.DEGREE)._value))
ang_type_i += 1
else:
warn("Found unimplemented angle type for LAMMPS!")
logger.warn("Found unimplemented angle type for LAMMPS!")
continue

angle_list.append('{0:-6d} {1:6d} {2:6d} {3:6d} {4:6d}\n'.format(
Expand All @@ -792,14 +783,10 @@ def write(self, data_file, unit_set='real', verbose=False):

angle_style.add(style)
if len(angle_style) > 1:
warn("More than one angle style found!")
if verbose:
print " Done. ({0:.2f} s)".format(time.time() - start)
logger.warn("More than one angle style found!")

# dihedrals
if verbose:
start = time.time()
print " Writing dihedrals..."
logger.debug(" Writing dihedrals...")

for j, dihedral in enumerate(mol_type.dihedralForceSet.itervalues()):
atomtype1 = molecule._atoms[dihedral.atom1 - 1].bondtype
Expand Down Expand Up @@ -893,7 +880,7 @@ def write(self, data_file, unit_set='real', verbose=False):
# If the 6th and/or 7th coefficients are non-zero, we decompose
# the dihedral into multiple CHARMM style dihedrals.
else:
warn("Found unsupported dihedral style.")
logger.warn("Found unsupported dihedral style.")
continue
"""
for n, coeff in enumerate(coefficients):
Expand Down Expand Up @@ -948,17 +935,13 @@ def write(self, data_file, unit_set='real', verbose=False):
" dihedrals to be of types ImproperHarmonic"
" or DihedralTrig.")
if len(dihedral_style) > 1:
warn("More than one dihedral style found!")
logger.warn("More than one dihedral style found!")
if len(improper_style) > 1:
warn("More than one improper style found!")
if verbose:
print " Done. ({0:.2f} s)".format(time.time() - start)
logger.warn("More than one improper style found!")

# atom specific information
x_min = y_min = z_min = np.inf
if verbose:
start = time.time()
print " Writing atoms..."
logger.debug(" Writing atoms...")
for molecule in mol_type.moleculeSet:
for atom in molecule._atoms:
# type, mass and pair coeffs
Expand Down Expand Up @@ -999,10 +982,6 @@ def write(self, data_file, unit_set='real', verbose=False):
atom._velocity[0].in_units_of(self.VEL)._value,
atom._velocity[1].in_units_of(self.VEL)._value,
atom._velocity[2].in_units_of(self.VEL)._value))
if verbose:
print " Done. ({0:.2f} s)".format(time.time() - start)
if verbose:
print " Done. ({0:.2f} s)".format(time.time() - mol_start)

# Write the actual data file.
with open(data_file, 'w') as f:
Expand Down

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