forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5712 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
46104f1588
commit
49b72ac36e
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@ -5,9 +5,12 @@ generating LAMMPS structure files:
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- h2.pl: rectangular lattice of hydrogen atoms
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- Diamond.pl: diamond A4 box
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- Li-hydride: Lithium hydride solid box
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- Li-solid: Lithium solid box
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- Li-solid: Lithium solid box (Li-solid-angstromg produces data file in Angstroms)
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- Uniform-electron-gas.pl: uniform electron gas on an NaCl lattice
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- bohr2ang.py: converts an eFF structure file described in bohr to
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its corresponding version in Angstroms
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And other useful scripts for processing pEFF related information are
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included, such as:
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@ -12,8 +12,8 @@ ajaramil@wag.caltech.edu
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Project: pEFF
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Version: August 2009
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Usage: python VMD-input.py lammps_dump_filename radii_column_number
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Example: python VMD-input.py dump.lammpstrj 6
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Usage: python VMD-input.py lammps_dump_filename radii_column xpos_column
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Example: python VMD-input.py dump.lammpstrj 5 6
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1. Extracts the electron radii from a lammps trajectory dump into %s.out
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2. Creates %s.xyz file
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@ -31,17 +31,28 @@ if __name__ == '__main__':
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# if no input, print help and exit
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if len(sys.argv) < 2:
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print "Usage: python VMD-input.py lammps_dump_filename radii_column_number\n"
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print "Usage: python VMD-input.py lammps_dump_filename radii_column xpos_column\n"
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sys.exit(1)
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else:
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infile=sys.argv[1]
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workdir=os.getcwd()
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tools=sys.argv[0].split('VMD-input.py')[0]
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# set defaults
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outfile = infile.split('.')[0]
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if len(sys.argv) == 2:
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print sys.argv
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if len(sys.argv) == 4:
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column = int(sys.argv[2])
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else:
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column=6 # default = radius for dump -> id type x y z spin radius
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xpos = int(sys.argv[3])
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print "Assuming xpos=eradius+1"
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elif len(sys.argv) == 3:
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column = int(sys.argv[2])
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xpos = column+1
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print "Assuming xpos=eradius+1"
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elif len(sys.argv) == 2:
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column=5 # default = radius for dump -> id type q spin eradius x y z
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xpos=6
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else: print "Incorrect number of arguments"
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# check for input:
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opts, argv = getopt(sys.argv[1:], 'c:o:ha')
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@ -54,12 +65,12 @@ if __name__ == '__main__':
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outfile=arg
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if opt == '-c': # select column from lammpstrj file to tabulate
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column=int(arg)
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print column,xpos
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makeradii(infile,outfile+".out",column,True)
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lmp2xyz(infile,outfile+".xyz")
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lmp2xyz(infile,outfile+".xyz",xpos)
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print "Creating %s file ..."%(outfile+".vmd")
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os.system("cat %s | sed 's/xyzfile/%s/' > %s"%("radii.vmd",outfile+".xyz","temp"))
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os.system("cat %s | sed 's/radiifile/%s/' > %s; rm temp"%("temp",outfile+".out",outfile+".vmd"))
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os.system("cat %s | sed 's/xyzfile/%s/' > %s"%(tools+"radii.vmd",outfile+".xyz","temp"))
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os.system("cat %s | sed 's/radiifile/%s/' > %s; rm temp"%("temp",outfile+".out",workdir+'/'+outfile+".vmd"))
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print "Done !! (you can now source %s using VMD's console) \n"%(outfile+".vmd")
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print "NOTE: In VMD, set graphics representation for electrons to transparency,"
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@ -12,6 +12,8 @@ Version: August 2009
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Reads in an eff .cfg file and produces the corresponding lammps data and input files
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NOTE: Unsupported functions will be reported in the output log
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12/2010: Added support for fixed-core and pseudo-core structures
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"""
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# import essentials:
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@ -38,15 +40,31 @@ units electron
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newton on
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boundary %s
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atom_style hybrid charge electron
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atom_style electron
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read_data data.${sname}
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pair_style eff/cut %s
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pair_coeff * *
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compute energies all pair eff/cut
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variable eke equal c_energies[1]
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variable epauli equal c_energies[2]
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variable estatics equal c_energies[3]
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variable errestrain equal c_energies[4]
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communicate single vel yes
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compute peratom all stress/atom
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compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
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variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
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compute effTemp all temp/eff
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compute effPress all pressure effTemp
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thermo %s
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thermo_style multi
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thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
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thermo_modify temp effTemp press effPress
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"""
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#%(date,name,boundary,cutoff,period)
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@ -55,7 +73,7 @@ minimize="""
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min_style cg
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dump 1 %s xyz %s ${sname}.min.xyz
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dump 2 %s custom %s ${sname}.min.lammpstrj id type x y z radius fx fy fz rf
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dump 2 %s custom %s ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce
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min_modify line quadratic
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minimize 0 1.0e-5 %s %s
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@ -77,7 +95,7 @@ timestep %s
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fix %s
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dump 1 %s custom %s ${sname}.%s.lammpstrj id type x y z spin radius
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dump 1 %s custom %s ${sname}.%s.lammpstrj id type q spin eradius x y z
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dump 2 %s custom %s ${sname}.%s.xyz
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run %s
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@ -114,8 +132,10 @@ def generate_lammps_input(infile):
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lines = fin.xreadlines()
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print 7*"\b"+"[DONE]"
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numcores=0
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numnuclei=0
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numelec=0
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cores={}
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nuclei={}
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electrons={}
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masses=[]
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@ -132,6 +152,9 @@ def generate_lammps_input(infile):
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if line.find("@params")==0:
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flag='params'
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continue
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elif line.find("@cores")==0:
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flag='cores'
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continue
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elif line.find("@nuclei")==0:
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flag='nuclei'
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continue
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@ -198,7 +221,7 @@ def generate_lammps_input(infile):
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if line.find("set_limit_stiffness")>=0:
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continue
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if line.find("output_position")>=0:
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dump_pos="dump\t1 all custom %s ${sname}.lammpstrj id type x y z spin radius "%(period)
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dump_pos="dump\t1 all custom %s ${sname}.lammpstrj id type q spin eradius x y z "%(period)
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if line.find("output_velocities")>=0:
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dump_pos+="vx vy vz "
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if line.find("output_energy_forces")>=0:
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@ -232,6 +255,22 @@ def generate_lammps_input(infile):
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cutoff=line.split()[2]
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continue
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if flag=='cores' and len(line)>1:
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numcores+=1
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ln=line.split()
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nc=' '.join(ln[0:3])
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q=ln[3]
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spin='3'
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radius=ln[4]
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m=q2m[int(float(q))]
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if m not in masses:
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masses.append(m)
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massstr+="%d %s\n"%(types,m)
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q2type[q]=types
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types+=1
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cores[numcores]=[nc,q,spin,radius]
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continue
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if flag=='nuclei' and len(line)>1:
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numnuclei+=1
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ln=line.split()
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@ -282,15 +321,17 @@ def generate_lammps_input(infile):
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print "Writing datafile to %s ... "%('data.'+infile),
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sys.stdout.flush()
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print "\b"*19+"General section ",
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datafile.writelines("Created using cfg2lammps (c) AJB-2009\n\n%d atoms\n%d atom types\n\n%s%s%s\n"%(numnuclei+numelec,types,xbound,ybound,zbound))
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datafile.writelines("Created using cfg2lammps (c) AJB-2009\n\n%d atoms\n%d atom types\n\n%s%s%s\n"%(numcores+numnuclei+numelec,types,xbound,ybound,zbound))
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print "\b"*19+"Masses section ",
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datafile.writelines(massstr)
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print "\b"*19+"Atoms section ",
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datafile.writelines("Atoms\n\n")
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for n in range(numcores):
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datafile.writelines("%d %d %2.2f %s %s %s\n"%(n+1,q2type[cores[n+1][1]],float(cores[n+1][1]),cores[n+1][2],cores[n+1][3],cores[n+1][0]))
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for n in range(numnuclei):
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datafile.writelines("%d %d %s %s 0 0.0\n"%(n+1,q2type[nuclei[n+1][1]],nuclei[n+1][0],nuclei[n+1][1]))
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datafile.writelines("%d %d %2.2f 0 0.0 %s\n"%(n+numcores+1,q2type[nuclei[n+1][1]],float(nuclei[n+1][1]),nuclei[n+1][0]))
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for e in range(numelec):
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datafile.write("%d %d %s 0.0 %s %s\n"%(e+numnuclei+1,types,electrons[e+1][0],electrons[e+1][1],electrons[e+1][2]))
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datafile.write("%d %d 0.0 %s %s %s\n"%(e+numnuclei+numcores+1,types,electrons[e+1][1],electrons[e+1][2],electrons[e+1][0]))
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print "\b"*19+"Velocities section\n",
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datafile.writelines(vels)
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datafile.writelines("\n")
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@ -11,9 +11,9 @@ Version: August 2009
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Extracts the electron radii from a lammps trajectory dump of style custom:
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dump 1 all custom period dump_file id type x y z spin radius ...
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dump 1 all custom period dump_file id type q spin eradius x y z...
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NOTE: The radius must be the 6th column per trajectory entry in the dump file
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NOTE: The radius must be the 5th column per trajectory entry in the dump file
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"""
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@ -45,7 +45,7 @@ def makeradii(infile):
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tmp=open("atoms",'r')
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atoms=int(tmp.readlines()[1].split()[0])
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tmp.close()
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os.system("rm -rf frames atoms")
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os.system("rm -rf frames atoms lines")
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arry=numpy.zeros((atoms,frames),dtype=float)
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framecnt=0
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header=9
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@ -59,8 +59,8 @@ def makeradii(infile):
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elif (i >= lo) and (i < hi):
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lparse=line.split()
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id=int(lparse[0])
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r=float(lparse[6])
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if (r!=0):
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r=float(lparse[4])
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if (r!=0.0):
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arry[id-1][framecnt]=r
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if (framecnt==0): ecount+=1
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if (i==lo+1):
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@ -11,9 +11,9 @@ Version: August 2009
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Extracts the electron radii from a lammps trajectory dump of style custom:
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dump 1 all custom period dump_file id type x y z spin radius ...
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dump 1 all custom period dump_file id type q spin eradius x y z...
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NOTE: The radius must be the 6th column per trajectory entry in the dump file
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NOTE: The radius must be the 5th column per trajectory entry in the dump file
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"""
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@ -59,7 +59,7 @@ def makeradii(infile):
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elif (i >= lo) and (i < hi):
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lparse=line.split()
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id=int(lparse[0])
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r=float(lparse[6])
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r=float(lparse[4])
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if (r!=0):
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arry[id-1][framecnt]=r
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if (framecnt==0): ecount+=1
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@ -87,7 +87,7 @@ def makeradii(infile):
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fout.writelines("%f\t"%(arry[a][f]))
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fout.writelines("\n")
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print
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print "DONE .... GOODBYE !!"
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print "Done !! (generated radii/frame table) \n"
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fout.close()
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fin.close()
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@ -11,7 +11,7 @@ Version: August 2009
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Extracts the electron radii from a lammps trajectory dump of style custom:
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dump 1 all custom period dump_file id type x y z spin radius ...
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dump 1 all custom period dump_file id type spin eradius x y z ...
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NOTE: The radius must be the "column" per trajectory entry in the dump file
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@ -59,7 +59,7 @@ def makeradii(infile,outfile,column,True):
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elif (i >= lo) and (i < hi):
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lparse=line.split()
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id=int(lparse[0])
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r=float(lparse[column])
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r=float(lparse[column-1])
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if (r!=0):
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arry[id-1][framecnt]=r
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if (framecnt==0): ecount+=1
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@ -96,7 +96,7 @@ if __name__ == '__main__':
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# set defaults
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outfile = ""
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flag_all = False
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column=6 # default = radius
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column=5 # default = radius
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# check for input:
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opts, argv = getopt(sys.argv[1:], 'c:o:ha')
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@ -15,15 +15,35 @@ Usage: python lmp2xyz.py lammps_dump_filename xyz_filename
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"""
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import os, sys
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from math import log10
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from math import log10,floor
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from numpy import zeros
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mass={"1.00794":"H","4.002602":"He","6.941":"Li","9.012182":"Be","10.811":"B","12.0107":"C","1.00":"Au","0.0005486":"Au"}
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masses={"1.00794":"H","4.002602":"He","6.941":"Li","9.012182":"Be","10.811":"B","12.0107":"C","1.00":"Au","0.0005486":"Au"}
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mass_floor={1:"H",4:"He",6:"Li",9:"Be",10:"B",12:"C",0:"Au",28:"Si"}
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def lmp2xyz(lammps,xyz):
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def lmp2xyz(lammps,xyz,xpos):
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print "\nGenerating %s file"%(xyz)
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fin=open(lammps,'r')
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fout=open(xyz,'w')
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data=raw_input("Do you have a corresponding data file? please enter filename or 'n': ")
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count=1
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if data!='n':
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dataf=open(data,'r')
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datafile=dataf.readlines()
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dataf.close()
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for line in datafile:
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if line.find("atom types")>=0:
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numtypes=int(line.split()[0])
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mass=zeros(numtypes,dtype=float)
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elif line.find("Masses")>=0:
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count+=1+datafile.index(line)
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elif line.find("Atoms")>=0:
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break
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for i in range(numtypes):
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mass[i]=float(datafile[count].split()[1])
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count+=1
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else:
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print "\nWill continue without a data file specification"
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header=9
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lines=fin.readlines()
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numatoms=lines[3].split()[0]
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@ -31,13 +51,15 @@ def lmp2xyz(lammps,xyz):
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tmp=open('lines','r')
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tlines=tmp.readline()
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tmp.close()
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os.system("rm lines")
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flines=int(tlines.split()[0])
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snaps=flines/(int(numatoms)+header)
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countsnap=1
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coords=zeros((int(numatoms),4),dtype=float)
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if data!='n': coords={}
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else: coords=zeros((int(numatoms),4),dtype=float)
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sys.stdout.write("Writing [%d]: "%(snaps))
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sys.stdout.flush()
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read_atoms=1
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read_atoms=0
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for line in lines:
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if line.find('ITEM: TIMESTEP')==0:
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read_atom_flag=False
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@ -53,14 +75,23 @@ def lmp2xyz(lammps,xyz):
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read_atoms+=1
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parse=line.split()
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if parse[0]!="":
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# print [mass_floor[int(floor(mass[int(parse[1])-1]))],float(parse[xpos-1]),float(parse[xpos]),float(parse[xpos+1])]
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if data!='n':
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if mass[int(parse[1])-1]==1.0:
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type='Au'
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else:
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type=mass_floor[int(floor(mass[int(parse[1])-1]))]
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coords[int(parse[0])-1]=[type,float(parse[xpos-1]),float(parse[xpos]),float(parse[xpos+1])]
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else:
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coords[int(parse[0])-1][0]=int(parse[1])
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coords[int(parse[0])-1][1]=float(parse[2])
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coords[int(parse[0])-1][2]=float(parse[3])
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coords[int(parse[0])-1][3]=float(parse[4])
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coords[int(parse[0])-1][1]=float(parse[xpos-1])
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coords[int(parse[0])-1][2]=float(parse[xpos])
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coords[int(parse[0])-1][3]=float(parse[xpos+1])
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if read_atoms==int(numatoms):
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read_atoms=0
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for i in range(int(numatoms)):
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fout.writelines("%d %2.4f %2.4f %2.4f\n"%(coords[i][0],coords[i][1],coords[i][2],coords[i][3]))
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if data!='n': fout.writelines("%s %2.4f %2.4f %2.4f\n"%(coords[i][0],coords[i][1],coords[i][2],coords[i][3]))
|
||||
else: fout.writelines("%d %2.4f %2.4f %2.4f\n"%(coords[i][0],coords[i][1],coords[i][2],coords[i][3]))
|
||||
|
||||
print "\nDone converting to xyz!!\n"
|
||||
fin.close()
|
||||
|
|
@ -76,6 +107,8 @@ if __name__ == '__main__':
|
|||
|
||||
inputfile=sys.argv[1]
|
||||
outfile=sys.argv[2]
|
||||
|
||||
lmp2xyz(inputfile,outfile.split()[0])
|
||||
if len(sys.argv)==4:
|
||||
xpos=sys.arv[3]-1
|
||||
else: xpos=5
|
||||
lmp2xyz(inputfile,outfile.split()[0],xpos)
|
||||
|
||||
|
|
|
|||
|
|
@ -171,7 +171,7 @@ proc do_radii {args} {
|
|||
foreach elec $data_array(0) r $data_array($fr) {
|
||||
set s [atomselect $molid "index [expr {$elec -1}]"]
|
||||
#set nr [expr {exp($r)}]
|
||||
set nr $r
|
||||
set nr [expr $r*1.5]
|
||||
$s set radius $nr
|
||||
$s delete
|
||||
#puts stderr "$fr $elec $nr"
|
||||
|
|
@ -192,9 +192,6 @@ global data_array molid
|
|||
set xyz xyzfile
|
||||
set data radiifile
|
||||
|
||||
# switch default rep to VDW.
|
||||
mol default style VDW
|
||||
|
||||
# load nuclear and electron xyz trajectory
|
||||
#set xyz [lindex $::argv 0]
|
||||
|
||||
|
|
@ -202,7 +199,35 @@ mol default style VDW
|
|||
#set datafile [lindex $::argv 1]
|
||||
|
||||
set molid [mol new $xyz waitfor all]
|
||||
mol modstyle 0 [molinfo top] VDW 1.0 32.0
|
||||
#mol modstyle 0 [molinfo top] VDW 0.2 32.0
|
||||
|
||||
set s [atomselect $molid "all"]
|
||||
$s set radius 0.1
|
||||
$s delete
|
||||
|
||||
color Display Background white
|
||||
display projection orthographic
|
||||
|
||||
# switch default rep to VDW.
|
||||
mol default style VDW
|
||||
mol delrep 0 $molid
|
||||
mol selection "name H He Li Be B C Si"
|
||||
mol addrep $molid
|
||||
mol modstyle 0 $molid VDW 2.0 32.0
|
||||
# spin +1
|
||||
mol material Transparent
|
||||
mol selection "name Au"
|
||||
mol addrep $molid
|
||||
mol modstyle 1 $molid VDW 0.4 32.0
|
||||
# spin -1
|
||||
#mol material Transparent
|
||||
mol selection "name Tl"
|
||||
mol addrep $molid
|
||||
mol modstyle 2 $molid VDW 0.4 32.0
|
||||
mol material Opaque
|
||||
mol selection "name H He Li Be B C Si"
|
||||
mol addrep $molid
|
||||
mol modstyle 3 $molid DynamicBonds 1.6 0.1 32
|
||||
|
||||
puts "Starting ..."
|
||||
readFile $data
|
||||
|
|
|
|||
Loading…
Reference in New Issue