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# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
GromacsLog.py
Parse the .log file output of the GROMACS mdrun program, specifically
during conjugate gradients minimization. Note the energy values for
various components as they change, and report their final values.
@author: Eric M
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
GROMACS is not very computer friendly about its output formats. In
this case, table headings and values appear on alternate lines, and
which ones are included varies from run to run.
Sample output:
Configuring nonbonded kernels...
Testing ia32 SSE2 support... present.
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond Harmonic Pot. LJ-14 Coulomb-14 LJ (SR)
1.67136e+01 3.91076e+01 6.14294e-01 0.00000e+00 4.51586e+01
Coulomb (SR) Potential Kinetic En. Total Energy Temperature
0.00000e+00 1.01594e+02 0.00000e+00 1.01594e+02 0.00000e+00
Pressure (bar)
0.00000e+00
F-max = 1.11581e+01 on atom 237
F-Norm = 7.33720e+01
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond Harmonic Pot. LJ-14 Coulomb-14 LJ (SR)
1.65284e+01 3.88862e+01 6.14476e-01 0.00000e+00 4.51403e+01
Coulomb (SR) Potential Kinetic En. Total Energy Temperature
0.00000e+00 1.01169e+02 0.00000e+00 1.01169e+02 0.00000e+00
Pressure (bar)
0.00000e+00
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond Harmonic Pot. LJ (SR) Coulomb (SR) Potential
1.96551e+00 1.16216e+00 0.00000e+00 0.00000e+00 3.12768e+00
Kinetic En. Total Energy Temperature Pressure (bar)
0.00000e+00 3.12768e+00 0.00000e+00 0.00000e+00
"""
import foundation.env as env
from utilities.Log import quote_html, orangemsg
AVOGADRO = 6.022045e23 # particles/mol
class GromacsLog(object):
def __init__(self):
self.state = 0
self._resetColumns()
def addLine(self, line):
columns = line.split()
if (len(columns) == 3 and
columns[0] == 'Step' and
columns[1] == 'Time' and
columns[2] == 'Lambda'):
self._resetColumns()
self.state = 1
return
if (self.state == 1 and len(columns) == 3):
self.step = columns[0]
self.state = 2
return
if (self.state == 2 and len(columns) == 0):
self.state = 3
return
if (self.state == 3 and len(columns) == 2 and columns[0] == 'Energies'):
self.state = 4
return
if (self.state == 4):
if (len(columns) > 0):
self.state = 5
self.column_headers = self._extractColumns(line.rstrip())
return
else:
self._emitColumns()
self.state = 0
return
if (self.state == 5):
if (len(columns) == len(self.column_headers)):
self._addColumns(self.column_headers, columns)
self.state = 4
return
else:
self.state = 0 # this never happens
return
# Stepsize too small, or no change in energy.
# Converged to machine precision,
# but not to the requested precision Fmax < 0.006022
#
# Polak-Ribiere Conjugate Gradients did not converge to Fmax < 0.006022 in 100001 steps.
if (line.find("converge") >= 0 and line.find("Fmax") >= 0):
env.history.message("Energy (Bond, Strut, Nonbonded): (%f, %f, %f) zJ" %
(self.getBondEnergy(),
self.getHarmonicEnergy(),
self.getNonbondedEnergy()))
env.history.message("Total Energy %f zJ" % self.getTotalEnergy())
if (line.find("machine") >= 0 or line.find("did not") >= 0):
env.history.message(orangemsg(quote_html(line.rstrip())))
else:
env.history.message(quote_html(line.rstrip()))
return
def _extractColumns(self, line):
columns = []
while (len(line) >= 15):
col = line[:15]
line = line[15:]
columns.append(col.strip())
return columns
def _resetColumns(self):
self._values = {}
self.step = "-"
def _addColumns(self, headers, values):
for i in range(len(headers)):
key = headers[i]
value = values[i]
self._values[key] = value
def _emitColumns(self):
result = "%s: (%f + %f + %f) = %f zJ" % (self.step,
self.getBondEnergy(),
self.getHarmonicEnergy(),
self.getNonbondedEnergy(),
self.getTotalEnergy())
env.history.statusbar_msg(result)
def kJ_per_mol_to_zJ(self, kJ_per_mol):
joules = kJ_per_mol * 1000.0 / AVOGADRO
return joules * 1e21
def _getSingleEnergy(self, key):
if (self._values.has_key(key)):
try:
value = float(self._values[key])
except:
print "_getSingleEnergy(): malformed value for %s: '%s'" % (key, self._values[key])
value = 0.0
return self.kJ_per_mol_to_zJ(value)
return 0.0
def getBondEnergy(self):
return self._getSingleEnergy("Bond") + self._getSingleEnergy("Morse") + self._getSingleEnergy("Angle")
def getHarmonicEnergy(self):
return self._getSingleEnergy("Harmonic Pot.")
def getNonbondedEnergy(self):
return self._getSingleEnergy("LJ-14") + self._getSingleEnergy("LJ (SR)") + self._getSingleEnergy("Buck.ham (SR)")
def getTotalEnergy(self):
return self._getSingleEnergy("Total Energy")
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