/usr/share/viewmol/tests/autotest.py is in viewmol 2.4.1-24+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#*******************************************************************************
# *
# Viewmol *
# *
# A U T O T E S T . P Y *
# *
# Copyright (c) Joerg-R. Hill, October 2003 *
# *
#*******************************************************************************
#
# $Id: autotest.py,v 1.1 2003/11/07 13:21:02 jrh Exp $
# $Log: autotest.py,v $
# Revision 1.1 2003/11/07 13:21:02 jrh
# Initial revision
#
#
import fnmatch
import os
import sys
import string
import viewmol
import molecule
import label
import light
import energylevels
import history
import spectrum
import time
class autotest:
label1=None
label2=None
mol=[]
xPos=0
yPos=0
def run(self):
viewmol.showWarnings(viewmol.__dict__['OFF'])
self.label1=label.label()
size=viewmol.getWindowSize()
self.xPos=20
self.yPos=size[1]-20
self.label1.text("Automatic tests")
self.label1.setColor(0.0, 0.0, 1.0, 0.0)
self.label2=label.label()
viewmolpath=os.getenv("VIEWMOLPATH")
for file in ["examples/turbomole/control", "examples/gulp/urea.out", "examples/discover/benzene.cor", "examples/dmol/quartz.outmol", "examples/gamess/c10h8n2.out", "examples/gaussian/mmdc1.log", "examples/mopac/adamantane.out", "examples/pqs/cpcpm.out", "examples/pdb/gpc.pdb"]:
self.testMolecule(viewmolpath + "/" + file)
self.createMolecule()
self.thermodynamics()
self.label2.delete()
self.label1.delete()
fps=viewmol.getFramesPerSecond()
viewmol.write("On average " + str(fps) + " frames per second were drawn.\n")
viewmol.write("Viewmol will be terminated in 5 seconds ...")
self.redrawWait(5)
viewmol.quit()
def testMolecule(self, file):
try:
viewmol.load(file)
except ValueError:
return
labels=viewmol.getLabels()
if (len(labels) != 2):
viewmol.quit()
mol=viewmol.getMolecules()
if (len(mol) == 1):
self.label1.translate(self.xPos, self.yPos, 0)
self.label2.translate(self.xPos, self.yPos-20, 0)
self.label1.text("Automatic tests: " + file)
self.drawingModeTest(mol[0])
self.moleculeTest(mol[0])
self.label1.translate(20, 40, 0)
self.label2.translate(20, 20 ,0)
spect=mol[0].getSpectrum()
if (spect != None):
self.spectrumTest(mol[0], spect)
del spect
levels=mol[0].getEnergyLevels()
if (levels != None):
self.energyLevelsTest(mol[0], levels)
del levels
hist=mol[0].getHistory()
if (hist != None):
self.historyTest(mol[0], hist)
del hist
self.atomTest(mol[0])
self.elementTest(mol[0])
for i in ['car', 'arc', 'mol', 'tm']:
viewmol.save(mol[0], "test.file", i)
os.unlink("test.file")
self.testSaving(viewmol, "molecule.test")
viewmol.delete(mol[0])
def drawingModeTest(self, mol):
self.label2.text("Drawing mode tests")
for i in ['WIREMODEL', 'STICKMODEL', 'BALLMODEL', 'CPKMODEL']:
viewmol.model(viewmol.__dict__[i])
viewmol.redraw()
for i in ['DOT', 'LINE', 'SURFACE']:
viewmol.drawingMode(viewmol.__dict__[i])
viewmol.redraw()
for i in ['PERSPECTIVE', 'ORTHO']:
viewmol.projection(viewmol.__dict__[i])
viewmol.redraw()
self.label2.text("Drawing mode tests" + ": " + "Sphere resolution")
light=viewmol.getLights()
light[0].switch(viewmol.__dict__['OFF'])
for i in range(4, 30, 2):
viewmol.sphereResolution(i)
light[1].rotate(0, 10*i, 0)
viewmol.redraw()
light[0].switch(viewmol.__dict__['ON'])
self.label2.text("Drawing mode tests" + ": " + "Line width")
viewmol.model(viewmol.__dict__['WIREMODEL'])
for i in range(1, 5):
viewmol.lineWidth(i)
viewmol.redraw()
viewmol.lineWidth(0)
# viewmol.projection(viewmol.__dict__['PERSPECTIVE'])
self.label2.text("Drawing mode tests" + ": " + "Colors and labels")
viewmol.labelAtoms(viewmol.__dict__['ON'])
color=viewmol.groundColor()
viewmol.groundColor(0.0, 1.0, 0.0)
self.redrawWait(2)
viewmol.groundColor(color[0], color[1], color[2])
color=viewmol.backgroundColor()
viewmol.backgroundColor(0.0, 0.0, 0.0)
self.redrawWait(2)
viewmol.backgroundColor(color[0], color[1], color[2])
viewmol.labelAtoms(viewmol.__dict__['OFF'])
viewmol.redraw()
def moleculeTest(self, mol):
self.label2.text("Molecule tests" + ": " + "Rotation")
for i in range(0, 360, 5):
mol.rotate(i, 0, 0)
for i in range(0, 360, 5):
mol.rotate(0, i, 0)
for i in range(0, 360, 5):
mol.rotate(0, 0, i)
mol.rotate(0, 0, 0)
self.label2.text("Molecule tests" + ": " + "Translation and forces")
mol.showForces(viewmol.__dict__['ON'])
for i in range(0, 5):
mol.translate(i, 0, 0)
for i in range(0, 5):
mol.translate(0, i, 0)
for i in range(0, 2):
mol.translate(0, 0, -i)
hasCell=1
try:
mol.unitCell(viewmol.__dict__['OFF'])
except ValueError:
hasCell=0
if hasCell == 1:
mol.unitCell(viewmol.__dict__['ON'], 2, 2, 2)
self.redrawWait(2)
mol.unitCell(viewmol.__dict__['ON'], 1, 1, 1)
mol.millerPlane(viewmol.__dict__['ON'], 1, 1, 1)
self.redrawWait(2)
mol.millerPlane(viewmol.__dict__['OFF'])
mol.showForces(viewmol.__dict__['OFF'])
mol.translate(-5, -5, 2)
atoms=mol.getAtoms()
bonds=mol.getBonds()
title=mol.title()
self.label2.text("Molecule tests" + ": " + str(len(atoms)) + " atoms and " + str(len(bonds)) + " bonds found in molecule " + title)
self.redrawWait(2)
l=mol.bondAverage(atoms[0])
self.label2.text("Molecule tests" + ": " + "The average bond length for atom 1 is " + str("%.3f" % l) + " Å.")
self.redrawWait(2)
l=mol.bondLength(atoms[bonds[0][0]], atoms[bonds[0][1]])
self.label2.text("Molecule tests" + ": " + "The bond between atom " + str(bonds[0][0]+1) + " and " + str(bonds[0][1]+1) + " is " + str("%.3f" % l) + " Å long.")
self.redrawWait(2)
self.label2.text("Molecule tests" + ": " + "The bond between atom " + str(bonds[0][0]+1) + " and " + str(bonds[0][1]+1) + " is now " + str("%.3f" % (l+1.0)) + " Å long.")
mol.bondLength(atoms[bonds[0][0]], atoms[bonds[0][1]], l+1.0, 'Ang')
self.redrawWait(2)
mol.bondLength(atoms[bonds[0][0]], atoms[bonds[0][1]], l, 'Ang')
found=0
for i in range(1, len(bonds)):
for j in range(i+1, len(bonds)):
if bonds[i][0] == bonds[j][0] or bonds[i][1] == bonds[j][1] or bonds[i][0] == bonds[j][1] or bonds[i][1] == bonds[j][0]:
if bonds[i][0] == bonds[j][0]:
l=mol.bondAngle(atoms[bonds[i][1]], atoms[bonds[i][0]], atoms[bonds[j][1]])
self.label2.text("Molecule tests" + ": " + "The bond angle formed by atoms " + str(bonds[i][1]+1) + ", " + str(bonds[i][0]+1) + " and " + str(bonds[j][1]+1) + " is " + str("%.1f" % l) + " deg.")
elif bonds[i][1] == bonds[j][1]:
l=mol.bondAngle(atoms[bonds[i][0]], atoms[bonds[i][1]], atoms[bonds[j][0]])
self.label2.text("Molecule tests" + ": " + "The bond angle formed by atoms " + str(bonds[i][0]+1) + ", " + str(bonds[i][1]+1) + " and " + str(bonds[j][0]+1) + " is " + str("%.1f" % l) + " deg.")
elif bonds[i][0] == bonds[j][1]:
l=mol.bondAngle(atoms[bonds[i][1]], atoms[bonds[i][0]], atoms[bonds[j][0]])
self.label2.text("Molecule tests" + ": " + "The bond angle formed by atoms " + str(bonds[i][1]+1) + ", " + str(bonds[i][0]+1) + " and " + str(bonds[j][0]+1) + " is " + str("%.1f" % l) + " deg.")
else:
l=mol.bondAngle(atoms[bonds[i][0]], atoms[bonds[i][1]], atoms[bonds[j][1]])
self.label2.text("Molecule tests" + ": " + "The bond angle formed by atoms " + str(bonds[i][0]+1) + ", " + str(bonds[i][1]+1) + " and " + str(bonds[j][1]+1) + " is " + str("%.1f" % l) + " deg.")
self.redrawWait(2)
found=1
break
if found == 1:
break
for i in range(1, len(bonds)):
torsion=[-1, bonds[i][0], bonds[i][1], -1]
for j in range(1, len(bonds)):
if (bonds[i][0] == bonds[j][0]):
torsion[0]=bonds[j][1]
if (bonds[i][0] == bonds[j][1]):
torsion[0]=bonds[j][0]
if (bonds[i][1] == bonds[j][0]):
torsion[3]=bonds[j][1]
if (bonds[i][1] == bonds[j][1]):
torsion[3]=bonds[j][0]
if torsion[0] != -1 and torsion[3] != -1:
break
l=mol.torsionAngle(atoms[torsion[0]], atoms[torsion[1]], atoms[torsion[2]], atoms[torsion[3]])
if l <= 360.0:
self.label2.text("Molecule tests" + ": " + "The torsion angle formed by atoms " + str(torsion[0]+1) + ", " + str(torsion[1]+1) + ", " + str(torsion[2]+1) + ", and " + str(torsion[3]+1) + " is " + str("%.1f" % l) + " deg.")
self.redrawWait(2)
mol.torsionAngle(atoms[torsion[0]], atoms[torsion[1]], atoms[torsion[2]], atoms[torsion[3]], l+90.)
self.label2.text("Molecule tests" + ": " + "The torsion angle formed by atoms " + str(torsion[0]+1) + ", " + str(torsion[1]+1) + ", " + str(torsion[2]+1) + ", and " + str(torsion[3]+1) + " is now " + str("%.1f" % (l+90.)) + " deg.")
self.redrawWait(2)
mol.torsionAngle(atoms[torsion[0]], atoms[torsion[1]], atoms[torsion[2]], atoms[torsion[3]], l)
for i in ['ENTHALPY', 'ENTROPY', 'GIBBS_ENERGY', 'HEAT_CAPACITY']:
t=mol.getThermodynamics(molecule.__dict__[i], molecule.__dict__['TRANSLATION'])
r=mol.getThermodynamics(molecule.__dict__[i], molecule.__dict__['ROTATION'])
if i == 'ENTHALPY' or i == 'GIBBS_ENERGY':
p=mol.getThermodynamics(molecule.__dict__[i], molecule.__dict__['PV'])
else:
p=0
v=mol.getThermodynamics(molecule.__dict__[i], molecule.__dict__['VIBRATION'])
total=mol.getThermodynamics(molecule.__dict__[i], molecule.__dict__['TOTAL'])
self.label2.text("Molecule tests" + ": " + str(i) + " = " +str(t) + " + " + str(r) + " + " + str(p) + " + " + str(v) + " = " + str(total))
def spectrumTest(self, mol, spect):
waveNumbers=mol.getWavenumbers()
max=0
j=0
for i in range(1, len(waveNumbers)):
if waveNumbers[i][1] > max:
max=waveNumbers[i][1]
j=i
title=mol.title()
self.label2.text("Spectrum tests" + ": " + str(len(waveNumbers)) + " wave numbers found in molecule " + title)
spect.show()
spect.zoom(0, 0, 5000, 100)
spect.display(spectrum.__dict__['ARROWS'])
self.redrawWait(2)
self.label2.text("Spectrum tests")
spect.mode(j)
self.redrawWait(1)
for atom in mol.getAtoms():
if (atom.getElement().getSymbol() == 'H'):
atom.neutronScatteringFactor(1.0)
for i in ['ALLMODES', 'IRMODES', 'RAMANMODES', 'INSMODES', 'IRMODES']:
spect.type(spectrum.__dict__[i])
self.redrawWait(2)
for i in ['ANIMATE', 'ARROWS', 'DISTORT', 'ARROWS']:
spect.display(spectrum.__dict__[i])
amplitude=spect.amplitude()
for j in range(1, 3):
spect.amplitude(j*0.3)
self.redrawWait(2)
spect.amplitude(amplitude)
spect.deselect()
for i in ['LINES', 'GAUSSIANS']:
spect.style(spectrum.__dict__[i])
self.redrawWait(2)
sf=spect.scaleFactor()
spect.scaleFactor(0.9)
self.redrawWait(2)
spect.scaleFactor(sf)
for i in range(50, 1000, 50):
spect.zoom(i, 0, 5000-i, 100)
self.testSaving(spect, "spectrum.test")
spect.style(spectrum.__dict__['LINES'])
def energyLevelsTest(self, mol, levels):
self.label2.text("Energy level tests")
levels.show()
for i in ['HARTREE', 'KJ/MOL', 'EV', '1/CM']:
levels.unit(energylevels.__dict__[i])
self.redrawWait(2)
levels.mode(energylevels.__dict__['DENSITY_OF_STATES'])
viewmol.redraw()
r=levels.resolution()
levels.resolution(0.5)
self.redrawWait(2)
levels.resolution(r)
levels.mode(energylevels.__dict__['ENERGY_LEVELS'])
atoms=mol.getAtoms()
try:
self.label2.text("Energy level tests" + ": 1s basis function on atom 1")
mol.selectBasisfunction(atoms[0], "s", 1)
mol.showElectrons(molecule.__dict__['BASIS_FUNCTION'], 20, molecule.__dict__['IP_LINEAR'])
hasBasis=1
except ValueError:
self.label2.text("Energy level tests" + ": No basis functions found")
hasBasis=0
self.redrawWait(2)
energies=mol.getMOEnergies()
j=0
for i in energies:
if i[0] > 0.0:
break
j=j+1
levels.selectMO(j-1)
self.label2.text("Energy level tests" + ": HOMO: " + str(energies[j-1][0]) + " Hartrees")
if hasBasis == 1:
viewmol.isosurface(0.05)
mol.showElectrons(molecule.__dict__['MO'], 10, molecule.__dict__['IP_LINEAR'])
self.redrawWait(2)
levels.deselect()
self.label2.text("Energy level tests" + ": Testing saving")
self.testSaving(levels, "mo.test")
def historyTest(self, mol, hist):
self.label2.text("Optimization history tests")
hist.show()
hist.showEnergy(viewmol.__dict__['OFF'])
self.redrawWait(2)
hist.showGradient(viewmol.__dict__['OFF'])
hist.showEnergy(viewmol.__dict__['ON'])
self.redrawWait(2)
hist.showGradient(viewmol.__dict__['ON'])
hist.showScales(viewmol.__dict__['OFF'])
self.redrawWait(2)
hist.showScales(viewmol.__dict__['ON'])
nhist=hist.iteration()
for i in range(1, nhist):
hist.iteration(i)
self.redrawWait(1)
hist.animate(viewmol.__dict__['ON'])
hist.animate(viewmol.__dict__['OFF'])
hist.iteration(nhist)
self.testSaving(hist, "history.test")
def atomTest(self, mol):
atoms=mol.getAtoms()
name=atoms[0].getElement().getSymbol()
coord=atoms[0].coordinates()
line="%10.6f, %10.6f, %10.6f" % (coord[0], coord[1], coord[2])
self.label2.text("Atom tests" + ": Atom 1 is " + name + " at " + line)
viewmol.model(viewmol.__dict__['CPKMODEL'])
rad=atoms[0].radius()
atoms[0].radius(rad+1.0)
self.redrawWait(2)
atoms[0].radius(rad)
radScale=atoms[0].radiusScaleFactor()
for i in range(1, 5):
atoms[0].radiusScaleFactor(radScale+i*0.1)
self.redrawWait(2)
atoms[0].radiusScaleFactor(radScale)
atoms[0].replace('Fe')
self.redrawWait(2)
atoms[0].delete()
viewmol.model(viewmol.__dict__['WIREMODEL'])
def elementTest(self, mol):
atoms=mol.getAtoms()
elem=atoms[0].getElement()
symbol=elem.getSymbol()
self.label2.text("Element tests" + ": Changing colors for element " + symbol)
color=elem.darkColor()
elem.darkColor(0.0, 0.0, 0.0)
self.redrawWait(1)
elem.darkColor(color[0], color[1], color[2])
color=elem.lightColor()
elem.lightColor(1.0, 1.0, 1.0)
self.redrawWait(1)
elem.lightColor(color[0], color[1], color[2])
color=elem.emissionColor()
elem.emissionColor(0.0, 1.0, 0.0)
self.redrawWait(1)
elem.emissionColor(color[0], color[1], color[2])
color=elem.ambientColor()
elem.ambientColor(1.0, 1.0, 1.0)
self.redrawWait(1)
elem.ambientColor(color[0], color[1], color[2])
color=elem.specularColor()
elem.specularColor(1.0, 0.0, 0.0)
self.redrawWait(1)
elem.specularColor(color[0], color[1], color[2])
shin=elem.shininess()
elem.shininess(0)
self.redrawWait(1)
elem.shininess(shin)
tp=elem.transperancy()
elem.transperancy(0.5)
self.redrawWait(1)
elem.transperancy(tp)
del elem
del atoms
def createMolecule(self):
self.label1.text("Building new molecule")
mol=molecule.molecule()
mol.addAtom('C')
atoms=mol.getAtoms()
mol.addAtom('O', atoms[0])
mol.addAtom('H', atoms[0])
mol.addAtom('H', atoms[0])
mol.addAtom('H', atoms[0])
atoms=mol.getAtoms()
mol.addAtom('H', atoms[1])
for i in range(0, 360, 5):
mol.rotate(i, 0, 0)
viewmol.delete(mol)
def thermodynamics(self):
self.label1.text("Thermodynamics")
viewmolpath=os.getenv("VIEWMOLPATH")
molecule1=viewmol.load(viewmolpath + "/examples/reaction/hio3.outmol")
molecule1.reaction(molecule.__dict__['PRODUCT'])
molecule1.translate(-1.0, 1.0, 0.0)
molecule2=viewmol.load(viewmolpath + "/examples/reaction/i2.outmol")
molecule2.reaction(molecule.__dict__['REACTANT'])
molecule2.rotate(90.0, 0.0, 0.0)
molecule2.translate(1.0, 1.0, 0.0)
molecule3=viewmol.load(viewmolpath + "/examples/reaction/hno3.outmol")
molecule3.reaction(molecule.__dict__['REACTANT'])
molecule3.translate(-1.0, -1.0, 0.0)
molecule4=viewmol.load(viewmolpath + "/examples/reaction/no.outmol")
molecule4.reaction(molecule.__dict__['PRODUCT'])
molecule4.rotate(90.0, 0.0, 0.0)
molecule4.translate(1.0, -1.0, 0.0)
molecule5=viewmol.load(viewmolpath + "/examples/reaction/h2o.outmol")
molecule5.reaction(molecule.__dict__['PRODUCT'])
viewmol.showThermodynamics(viewmol.__dict__['REACTION'])
self.redrawWait(5)
for i in viewmol.getMolecules():
viewmol.delete(i)
def testSaving(self, object, file):
for i in ['TIFF', 'PNG', 'HPGL', 'POSTSCRIPT']:
self.label2.text("Save tests" + ": Saving as " + i)
try:
object.saveDrawing(viewmol.__dict__[i], file)
except IOError:
pass
os.unlink(file)
def redrawWait(self, duration):
viewmol.redraw()
time.sleep(duration)
def register(self, language):
viewmol.registerMenuItem("Automatic test")
#-------------------------
if __name__ == '__main__':
autotest().run()
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