def write_nh_header(f, desc, iter, spf, temp, workflow_fname, mmp_fname):
'''Writes the Nano-Hive Sim specification file, which is an XML file that describes the
simulation environment, plugin selection and plugin parameters.
'''
nh_home = get_nh_home()
#print "files_nh.write_nh_header(): Nano-Hive Home:", nh_home
# Write SimSpec header ########################################
f.write('<simulation>\n')
f.write(' <description>%s</description>\n' % desc)
f.write('\n')
f.write(' <parameter name="timeQuantumLength" value="%e" />\n' % spf)
f.write(' <parameter name="environmentTemperature" value="%d" />\n' %
temp)
f.write(' <parameter name="startIteration" value="0" />\n')
f.write(' <parameter name="iterations" value="%d" />\n' % iter)
f.write('\n')
f.write(' <simulationFlow file="%s">\n' % workflow_fname)
f.write(' <input name="inFile" type="nanorexMMP" file="%s" />\n' %
mmp_fname)
# This traverser is for the local machine.
f.write(' <traverser name="traverser" plugin="RC_Traverser" />\n')
def write_nh_mpqc_gd_rec(f):
nh_home = get_nh_home()
f.write('\n')
f.write(' <calculator name="physicalInteraction" plugin="REBO_MBM">\n')
f.write(' <parameter name="dataDirectory" value="%s/data/REBO_MBM" />\n' % nh_home)
f.write(' </calculator>\n')
def write_nh_mpqc_gd_rec(f):
nh_home = get_nh_home()
f.write('\n')
f.write(' <calculator name="physicalInteraction" plugin="REBO_MBM">\n')
f.write(
' <parameter name="dataDirectory" value="%s/data/REBO_MBM" />\n' %
nh_home)
f.write(' </calculator>\n')
def write_nh_mpqc_esp_plane_rec(f, esp_image, output_dir):
nh_home = get_nh_home()
cpnt = esp_image.center * 1e-10
centerPoint = (float(cpnt[0]), float(cpnt[1]), float(cpnt[2]))
#print "ESP Image CenterPoint =", centerPoint
npnt = cpnt + (esp_image.planeNorm * 1e-10)
# This is a temporary workaround until Brian fixes the normalPoint Y value issue (must be positive).
# This forces ESP Images to be oriented in the X-Z plane until it is fixed.
# Mark 050927.
# normalPoint = (0.0, 0.0, 1.0) + cpnt
normalPoint = (float(npnt[0]), float(npnt[1]), float(npnt[2])) # KEEP THIS!!!
#print "ESP Image NormalPoint =", normalPoint
resolution = esp_image.resolution
# print "ESP Image Resolution =", resolution
cutoffHeight = esp_image.image_offset * 1e-10
#print "ESP Image cutoffHeight =", cutoffHeight
cutoffWidth = esp_image.edge_offset * 1e-10
#print "ESP Image cutoffWidth =", cutoffWidth
outputLength = esp_image.width * 1e-10
#print "ESP Image outputLength =", outputLength
multi = esp_image.multiplicity
f.write('\n')
f.write(' <calculator name="espImage" plugin="MPQC_SClib">\n')
f.write(' <parameter name="logDirectory" value="%s/log" />\n' % nh_home)
f.write(' <parameter name="dataDirectory" value="%s/data/MPQC_SClib" />\n' % nh_home)
f.write(' <parameter name="basis" value="STO-3G" />\n')
f.write(' <parameter name="method" value="HF" />\n')
f.write(' <parameter name="desiredEnergyAccuracy" value="1.0e-5" />\n')
f.write(' <parameter name="multiplicity" value="%d" />\n' % multi)
f.write('\n')
f.write(' <parameter name="outputType" value="ESPplane" />\n')
f.write(' <parameter name="resolution" value="%d" />\n' % resolution)
f.write('\n')
f.write(' <parameter name="centerPoint" value="%.2e %.2e %.2e" />\n' % centerPoint)
f.write(' <parameter name="normalPoint" value="%.2e %.2e %.2e" />\n' % normalPoint)
f.write(' <parameter name="cutoffHeight" value="%.2e" />\n' % cutoffHeight)
f.write(' <parameter name="cutoffWidth" value="%.2e" />\n' % cutoffWidth)
f.write(' <parameter name="outputLength" value="%.2e" />\n' % outputLength)
f.write(' </calculator>\n')
f.write('\n')
f.write(' <result name="simResult" plugin="_ESP_Image">\n')
f.write(' <parameter name="outputFilename" value="%s\\%s.png" />\n' % (output_dir, esp_image.name))
f.write(' <parameter name="xaxisOrient" value="%d" />\n' % esp_image.xaxis_orient)
f.write(' <parameter name="yaxisOrient" value="%d" />\n' % esp_image.yaxis_orient)
f.write(' </result>\n')
def write_nh_mpqc_gd_rec(f):
nh_home = get_nh_home()
f.write('\n')
f.write(' <calculator name="qmDynamicsInteraction" plugin="MPQC_SClib">\n')
f.write(' <parameter name="logDirectory" value="%s/log" />\n' % nh_home)
f.write(' <parameter name="dataDirectory" value="%s/data/MPQC_SClib" />\n' % nh_home)
f.write(' <parameter name="basis" value="STO-3G" />\n')
f.write(' <parameter name="method" value="HF" />\n')
f.write(' <parameter name="gradientDynamics" value="yes" />\n')
f.write(' <parameter name="deltaTbyTau" value="1.0" />\n')
f.write(' </calculator>\n')
def write_nh_mpqc_gd_rec(f):
nh_home = get_nh_home()
f.write('\n')
f.write(
' <calculator name="qmDynamicsInteraction" plugin="MPQC_SClib">\n')
f.write(' <parameter name="logDirectory" value="%s/log" />\n' %
nh_home)
f.write(
' <parameter name="dataDirectory" value="%s/data/MPQC_SClib" />\n'
% nh_home)
f.write(' <parameter name="basis" value="STO-3G" />\n')
f.write(' <parameter name="method" value="HF" />\n')
f.write(' <parameter name="gradientDynamics" value="yes" />\n')
f.write(' <parameter name="deltaTbyTau" value="1.0" />\n')
f.write(' </calculator>\n')
def write_nh_povrayvideo_results_rec(f, output_dir, partname):
nh_home = get_nh_home()
# Need subdirectory for all the POV-Ray pov files.
# Also need to add lighting, scene setup, background color, etc.
f.write('\n')
f.write(' <result name="POVRayVideo" plugin="POVRayVideo">\n')
f.write(' <parameter name="outputInterval" value="1" />\n')
f.write(' <parameter name="lengthMultiplier" value="1e10" />\n')
f.write(' <parameter name="outputDirectory"\n')
f.write(' value="%s/povray" />\n' % output_dir)
f.write(' <parameter name="outputIdentifier" value="%s" />\n' % partname)
# POV-Ray template. Mark needs to write the include file for lighting and camera angle(s)
# and put that file in the appropriate place (outdir/povray).
f.write(' <parameter name="povTemplateFilename"\n')
f.write(' value="%s/data/pov.tmplt" />')
f.write(' <parameter name="mpegTemplateFilename"\n')
f.write(' value="%s/data/mpeg_encode.param.tmplt" />\n' % nh_home)
f.write(' </result>\n')
def write_nh_povrayvideo_results_rec(f, output_dir, partname):
nh_home = get_nh_home()
# Need subdirectory for all the POV-Ray pov files.
# Also need to add lighting, scene setup, background color, etc.
f.write('\n')
f.write(' <result name="POVRayVideo" plugin="POVRayVideo">\n')
f.write(' <parameter name="outputInterval" value="1" />\n')
f.write(' <parameter name="lengthMultiplier" value="1e10" />\n')
f.write(' <parameter name="outputDirectory"\n')
f.write(' value="%s/povray" />\n' % output_dir)
f.write(' <parameter name="outputIdentifier" value="%s" />\n' %
partname)
# POV-Ray template. Mark needs to write the include file for lighting and camera angle(s)
# and put that file in the appropriate place (outdir/povray).
f.write(' <parameter name="povTemplateFilename"\n')
f.write(' value="%s/data/pov.tmplt" />')
f.write(' <parameter name="mpegTemplateFilename"\n')
f.write(' value="%s/data/mpeg_encode.param.tmplt" />\n' % nh_home)
f.write(' </result>\n')
def write_nh_header(f, desc, iter, spf, temp, workflow_fname, mmp_fname):
'''Writes the Nano-Hive Sim specification file, which is an XML file that describes the
simulation environment, plugin selection and plugin parameters.
'''
nh_home = get_nh_home()
#print "files_nh.write_nh_header(): Nano-Hive Home:", nh_home
# Write SimSpec header ########################################
f.write ('<simulation>\n')
f.write(' <description>%s</description>\n' % desc)
f.write('\n')
f.write(' <parameter name="timeQuantumLength" value="%e" />\n' % spf)
f.write(' <parameter name="environmentTemperature" value="%d" />\n' % temp)
f.write(' <parameter name="startIteration" value="0" />\n')
f.write(' <parameter name="iterations" value="%d" />\n' % iter)
f.write('\n')
f.write(' <simulationFlow file="%s">\n' % workflow_fname)
f.write(' <input name="inFile" type="nanorexMMP" file="%s" />\n' % mmp_fname)
# This traverser is for the local machine.
f.write(' <traverser name="traverser" plugin="RC_Traverser" />\n')
def write_nh_mpqc_esp_plane_rec(f, esp_image, output_dir):
nh_home = get_nh_home()
cpnt = esp_image.center * 1e-10
centerPoint = (float(cpnt[0]), float(cpnt[1]), float(cpnt[2]))
#print "ESP Image CenterPoint =", centerPoint
npnt = cpnt + (esp_image.planeNorm * 1e-10)
# This is a temporary workaround until Brian fixes the normalPoint Y value issue (must be positive).
# This forces ESP Images to be oriented in the X-Z plane until it is fixed.
# Mark 050927.
# normalPoint = (0.0, 0.0, 1.0) + cpnt
normalPoint = (float(npnt[0]), float(npnt[1]), float(npnt[2])
) # KEEP THIS!!!
#print "ESP Image NormalPoint =", normalPoint
resolution = esp_image.resolution
# print "ESP Image Resolution =", resolution
cutoffHeight = esp_image.image_offset * 1e-10
#print "ESP Image cutoffHeight =", cutoffHeight
cutoffWidth = esp_image.edge_offset * 1e-10
#print "ESP Image cutoffWidth =", cutoffWidth
outputLength = esp_image.width * 1e-10
#print "ESP Image outputLength =", outputLength
multi = esp_image.multiplicity
f.write('\n')
f.write(' <calculator name="espImage" plugin="MPQC_SClib">\n')
f.write(' <parameter name="logDirectory" value="%s/log" />\n' %
nh_home)
f.write(
' <parameter name="dataDirectory" value="%s/data/MPQC_SClib" />\n'
% nh_home)
f.write(' <parameter name="basis" value="STO-3G" />\n')
f.write(' <parameter name="method" value="HF" />\n')
f.write(
' <parameter name="desiredEnergyAccuracy" value="1.0e-5" />\n')
f.write(' <parameter name="multiplicity" value="%d" />\n' % multi)
f.write('\n')
f.write(' <parameter name="outputType" value="ESPplane" />\n')
f.write(' <parameter name="resolution" value="%d" />\n' % resolution)
f.write('\n')
f.write(' <parameter name="centerPoint" value="%.2e %.2e %.2e" />\n' %
centerPoint)
f.write(' <parameter name="normalPoint" value="%.2e %.2e %.2e" />\n' %
normalPoint)
f.write(' <parameter name="cutoffHeight" value="%.2e" />\n' %
cutoffHeight)
f.write(' <parameter name="cutoffWidth" value="%.2e" />\n' %
cutoffWidth)
f.write(' <parameter name="outputLength" value="%.2e" />\n' %
outputLength)
f.write(' </calculator>\n')
f.write('\n')
f.write(' <result name="simResult" plugin="_ESP_Image">\n')
f.write(' <parameter name="outputFilename" value="%s\\%s.png" />\n' %
(output_dir, esp_image.name))
f.write(' <parameter name="xaxisOrient" value="%d" />\n' %
esp_image.xaxis_orient)
f.write(' <parameter name="yaxisOrient" value="%d" />\n' %
esp_image.yaxis_orient)
f.write(' </result>\n')
