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# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
PyrexSimulator.py - Wrapper around the pyrex/C ND-1 simulator code.
Responsible for maintaining references to strings which are passed
to the C code, and which end up referenced by variables defined in
src/sim/globals.c.
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
import os
import foundation.env as env
from platform_dependent.PlatformDependent import find_plugin_dir
_thePyrexSimulator = None
class _PyrexSimulator(object):
def __init__(self):
global _thePyrexSimulator
assert (_thePyrexSimulator is None)
_thePyrexSimulator = self
import sim # this import must not be done at toplevel
self.sim = sim.theSimulator()
ok, nd1_plugin_path = find_plugin_dir("NanoDynamics-1")
if (not ok):
env.history.redmsg("Error: can't find " + nd1_plugin_path)
nd1_plugin_path = "."
self.system_parameters_file = os.path.join(nd1_plugin_path, "sim-params.txt")
self.amber_bonded_parameters_file = os.path.join(nd1_plugin_path, "ffamber03bon.itp")
self.amber_nonbonded_parameters_file = os.path.join(nd1_plugin_path, "ffamber03nb.itp")
self.amber_charges_file = os.path.join(nd1_plugin_path, "ffamber03charge.itp")
def reInitialize(self):
self.sim.reinitGlobals()
self.sim.SystemParametersFileName = self.system_parameters_file
self.sim.AmberBondedParametersFileName = self.amber_bonded_parameters_file
self.sim.AmberNonbondedParametersFileName = self.amber_nonbonded_parameters_file
self.sim.AmberChargesFileName = self.amber_charges_file
def setup(self, mflag, filename):
self.inputFileName = filename
self.outputFileName = None
self.reInitialize()
if (mflag):
self.sim.ToMinimize = 1
self.sim.DumpAsText = 1
else:
self.sim.ToMinimize = 0
self.sim.DumpAsText = 0
self.sim.PrintFrameNums = 0
self.sim.InputFileName = self.inputFileName
def setOutputFileName(self, filename):
self.outputFileName = filename
def run(self, frame_callback = None, trace_callback = None):
if (self.outputFileName is None):
if (self.sim.DumpAsText):
outputExtension = "xyz"
else:
outputExtension = "dpb"
if (self.inputFileName.endswith(".mmp")):
self.outputFileName = self.inputFileName[:-3] + outputExtension
else:
self.outputFileName = self.inputFileName + "." + outputExtension
self.sim.OutputFileName = self.outputFileName
if (self.sim.DumpAsText):
self.sim.OutputFormat = 0
else:
self.sim.OutputFormat = 1
self.sim.go(frame_callback, trace_callback)
def getEquilibriumDistanceForBond(self, element1, element2, order):
self.reInitialize()
return self.sim.getEquilibriumDistanceForBond(element1, element2, order)
def thePyrexSimulator():
global _thePyrexSimulator
if (_thePyrexSimulator is None):
_thePyrexSimulator = _PyrexSimulator()
return _thePyrexSimulator
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