diff --git a/tools/README b/tools/README index 09696c4b85..0a08de51fe 100644 --- a/tools/README +++ b/tools/README @@ -18,6 +18,7 @@ ch2lmp convert CHARMM files to LAMMPS input chain create a data file of bead-spring chains data2xmovie convert a data file to a snapshot that xmovie can viz eam_generate generate EAM potential files +eff scripts for working with the EFF (electron force field) lmp2arc convert LAMMPS output to Accelrys Insight format lmp2cfg convert LAMMPS output to CFG files for AtomEye viz lmp2traj convert LAMMPS output to contour, density profiles diff --git a/tools/eff/README b/tools/eff/README new file mode 100644 index 0000000000..edc52edaa0 --- /dev/null +++ b/tools/eff/README @@ -0,0 +1,45 @@ +The directory structure_generators includes several scripts for +generating LAMMPS structure files: + +- Be-solid.pl: beryllium solid box +- h2.pl: rectangular lattice of hydrogen atoms +- Diamond.pl: diamond A4 box +- Li-hydride: Lithium hydride solid box +- Li-solid: Lithium solid box +- Uniform-electron-gas.pl: uniform electron gas on an NaCl lattice + +And other useful scripts for processing pEFF related information are +included, such as: + +- cfg2lammps.py: Python script for converting an eff cfg file into a + LAMMPS data/script file pair + +- lmp2radii.py/pyx: Python/Cython scripts for post-processing a lammps + trajectory to extract electron radii/frame. + +Note: the corresponding .c, and .so files are the c source and binary +library (loadable Python module) created by Cython automatically when +compiling lmp2radii.pyx in place with Cython (python setup.py +build_ext --inplace). + +- radii.vmd: a TCL script for adding radial changes per trajectory + frame to an xyz LAMMPS trajectory of an pEFF run. + +- lmp2any.py: Python scipt for extracting quantities from a custom + lammps dump + +- lmp2radii-col.py: Same as lmp2radii.py, but takes a column + descriptor for the radius + +- VMD-input.py: Automatically calls the necessary scripts to produce a + VMD ready script that loads variable radii into VMD + +NOTE: you must set the graphical representation in VMD to represent +electrons using transparency (this requires selecting and applying the +corresponding atom types). + +For further details see the descriptors in each file, or contact: +Andres Jaramillo-Botero: ajaramil@wag.caltech.edu + +Acknowledgments: Thanks to Axel Kohlmeyer (Temple Univ) for his help +with VMD. diff --git a/tools/eff/VMD-input.py b/tools/eff/VMD-input.py new file mode 100644 index 0000000000..2d6c5f7233 --- /dev/null +++ b/tools/eff/VMD-input.py @@ -0,0 +1,67 @@ +#!/usr/local/bin/python-2.5/bin/python + +import sys, os +from getopt import gnu_getopt as getopt + +Info=""" +Module name: VMD-input.py + +Author: (c) Andres Jaramillo-Botero +California Institute of Technology +ajaramil@wag.caltech.edu +Project: pEFF +Version: August 2009 + +Usage: python VMD-input.py lammps_dump_filename radii_column_number +Example: python VMD-input.py dump.lammpstrj 6 + +1. Extracts the electron radii from a lammps trajectory dump into %s.out +2. Creates %s.xyz file +3. Creates appropriate %.vmd file which can be sourced using TCL/TK in VMD + +""" + +from lmp2radii_col import makeradii +from lmp2xyz import lmp2xyz + +def printHelp(input): + Info%(input,input,input) + +if __name__ == '__main__': + + # if no input, print help and exit + if len(sys.argv) < 2: + print "Usage: python VMD-input.py lammps_dump_filename radii_column_number\n" + sys.exit(1) + else: + infile=sys.argv[1] + + # set defaults + outfile = infile.split('.')[0] + if len(sys.argv) == 2: + column = int(sys.argv[2]) + else: + column=6 # default = radius for dump -> id type x y z spin radius + + # check for input: + opts, argv = getopt(sys.argv[1:], 'c:o:ha') + + # read options + for opt, arg in opts: + if opt == '-h': # -h: print help + Info%(input,input,input) + if opt == '-o': # output file name + outfile=arg + if opt == '-c': # select column from lammpstrj file to tabulate + column=int(arg) + + makeradii(infile,outfile+".out",column,True) + lmp2xyz(infile,outfile+".xyz") + print "Creating %s file ..."%(outfile+".vmd") + os.system("cat %s | sed 's/xyzfile/%s/' > %s"%("radii.vmd",outfile+".xyz","temp")) + os.system("cat %s | sed 's/radiifile/%s/' > %s; rm temp"%("temp",outfile+".out",outfile+".vmd")) + print "Done !! (you can now source %s using VMD's console) \n"%(outfile+".vmd") + + print "NOTE: In VMD, set graphics representation for electrons to transparency," + print "and change the atom types in the xyz file according to your values," + print "for simplicity, they are set using the same mass sequence definition\nfrom your lammps data file\n" diff --git a/tools/eff/cfg2lammps.py b/tools/eff/cfg2lammps.py new file mode 100644 index 0000000000..4e200c9723 --- /dev/null +++ b/tools/eff/cfg2lammps.py @@ -0,0 +1,336 @@ +#!/usr/local/bin/python-2.5/bin/python + +Info=""" +Module name: cfg2lammps.py + +Author: (c) Andres Jaramillo-Botero +California Institute of Technology +ajaramil@wag.caltech.edu +Project: pEFF +Version: August 2009 + +Reads in an eff .cfg file and produces the corresponding lammps data and input files + +NOTE: Unsupported functions will be reported in the output log +""" + +# import essentials: +import sys, os +from math import log10 +from shutil import rmtree +from getopt import gnu_getopt as getopt +import numpy + +def printHelp(): + print Info + print "Usage: python cfg2lammps cfgfile\n" + return + +general=""" +# Created %s + +# General parameters + +variable sname index %s +log ${sname}.log + +units electron +newton on +boundary %s + +atom_style hybrid charge electron + +read_data data.${sname} + +pair_style eff/cut %s +pair_coeff * * + +thermo %s +thermo_style multi +""" +#%(date,name,boundary,cutoff,period) + +minimize=""" +# Minimization + +min_style cg +dump 1 %s xyz %s ${sname}.min.xyz +dump 2 %s custom %s ${sname}.min.lammpstrj id type x y z radius fx fy fz rf +min_modify line quadratic +minimize 0 1.0e-5 %s %s + +undump 1 +undump 2 +""" +#%(group,period,group,period,iterations,fcalls) + +single_pt=""" +# Single point energy + +run 0 +""" +dynamics=""" + +# %s Dynamics + +timestep %s + +fix %s + +dump 1 %s custom %s ${sname}.%s.lammpstrj id type x y z spin radius +dump 2 %s custom %s ${sname}.%s.xyz + +run %s + +unfix 1 +undump 1 +undump 2 +""" + +task={'single_pt':single_pt,'minimize':minimize,'dynamics':dynamics} + +q2m={1:'1.007940',2:'4.002602',3:'6.941000',4:'9.012182',5:'10.811000',6:'12.010700',7:'14.006700',8:'15.999400', + 9:'18.9984032',10:'20.179700',11:'22.98976928',12:'24.305000',13:'26.9815386',14:'28.085500',15:'30.973762', + 16:'32.065000',17:'35.453000',18:'39.948000'} + +def generate_lammps_input(infile): + + # Defaults values + ensemble={"nve":"1 %s nve/eff",'nvt':"1 %s nvt/eff %s %s %s %s",'npt':"1 %s npt/eff %s %s %s %s %s %s"} + boundary="f f f" + xbound="-1000.000 1000.0 xlo xhi\n" + ybound="-1000.000 1000.0 ylo yhi\n" + zbound="-1000.000 1000.0 zlo zhi\n" + cutoff=1000.0 + period="1" + emass=0 + vels="" + + datafile=open("data."+infile[:-4],'w') + scriptfile=open("in."+infile[:-4],'w') + + print "Reading %s ... [WAIT]"%infile, + fin = open(infile,'r') + lines = fin.xreadlines() + print 7*"\b"+"[DONE]" + + numnuclei=0 + numelec=0 + nuclei={} + electrons={} + masses=[] + massstr="Masses\n\n" + types=1 + q2type={} + Tflag=False # Default ensemble is NVE + steps='1000' + + print "Extracting run parameters from %s ... "%(infile), + for line in lines: + + # 1st level keywords + if line.find("@params")==0: + flag='params' + continue + elif line.find("@nuclei")==0: + flag='nuclei' + continue + elif line.find("@electrons")==0: + flag='electrons' + continue + elif line.find("@nuc_velocities")==0: + flag='n_vels' + continue + elif line.find("@elec_velocities")==0: + flag='e_vels' + continue + elif line.find("@nuc_masses")==0: + flag='n_mass' + continue + elif line.find("@elec_masses")==0: + flag='e_mass' + continue + elif line.find("@restraints")==0: + flag='restraints' + continue + + # 2nd level keywords + if flag=='params': + if line.find("calc")>=0: + op=line.split()[2] + if line.find("print_every")>=0: + period=line.split()[2] + if line.find("num_steps")>=0: + steps=line.split()[2] + if line.find("min_freeze")>=0: + setforce="velocity\t% set 0.0 0.0 0.0\nfix\tfreeze %s setforce 0.0 0.0 0.0"%(line.split()[2],line.split()[2]) + if line.find("thermostat")>=0: + tflag=True + #ensemble="fix\t1 all nvt/eff " + if line.find("start_temperature")>=0: + Tstart=line.split()[2] + #ensemble+=Tstart + if line.find("end_temperature")>=0: + Tstop=line.split()[2] + #ensemble+=Tstop + if line.find("andersen_coupling")>=0 or line.find("nose_hoover_coupling")>=0: + Tdamp=line.split()[2] + #ensemble+=Tdamp + if line.find("dt")>=0: + dt=line.split()[2] + if line.find("electron_mass")>=0: + emass=line.split()[2] + if line.find("adaptive_step_size")>=0: + continue + if line.find("adaptive_energy")>=0: + continue + if line.find("e_field_freq")>=0: + continue + if line.find("e_field_packet_duration")>=0: + continue + if line.find("e_field")>=0: + field=line.split()[2:5] + efield="fix\field all efield %s %s %s"%(field[0],field[1],field[2]) + if line.find("e_field_packet_duration")>=0: + continue + if line.find("set_limit")>=0: + continue # need to add this contraint + if line.find("set_limit_stiffness")>=0: + continue + if line.find("output_position")>=0: + dump_pos="dump\t1 all custom %s ${sname}.lammpstrj id type x y z spin radius "%(period) + if line.find("output_velocities")>=0: + dump_pos+="vx vy vz " + if line.find("output_energy_forces")>=0: + dump_pos="compute\tenergy all pe/atom\n"+dump_pos + dump_pos+="c_energy fx fy fz\n" + if line.find("output_restart")>=0: + restart="restart\t%s ${sname}.restart1 ${sname}.restart2"%(period) + if line.find("output_restraints")>=0: + continue + if line.find("ewald_re_cutoff")>=0 or line.find("ewald_autoset")>=0 or line.find("ewald_log_precision")>=0 or line.find("ewald_max_re")>=0 or \ + line.find("ewald_r_cutoff")>=0 or line.find("ewald_k_cutoff")>=0 or line.find("ewald_nuc_r")>=0: + continue + if line.find("periodic")>=0: + bounds=line.split()[2] + if bounds=="True": boundary="p p p" + elif bounds=="minimage_x": boundary="p f f" + elif bounds=="minimage_xy": boundary="p p f" + elif bounds=="minimage_y": boundary="f p f" + elif bounds=="minimage_xyz": boundary="p p p" + elif bounds=="minimage_z": boundary="f f p" + if line.find("x_bound")>=0: + xbnds=line.split()[2:4] + xbound="%s %s xlo xhi\n"%(xbnds[0],xbnds[1]) + if line.find("y_bound")>=0: + ybnds=line.split()[2:4] + ybound="%s %s ylo yhi\n"%(ybnds[0],ybnds[1]) + if line.find("z_bound")>=0: + zbnds=line.split()[2:4] + zbound="%s %s zlo zhi\n"%(zbnds[0],zbnds[1]) + if line.find("taper_cutoff")>=0: + cutoff=line.split()[2] + continue + + if flag=='nuclei' and len(line)>1: + numnuclei+=1 + ln=line.split() + np=' '.join(ln[0:3]) + q=ln[3] + m=q2m[int(float(q))] + if m not in masses: + masses.append(m) + massstr+="%d %s\n"%(types,m) + q2type[q]=types + types+=1 + nuclei[numnuclei]=[np,q] + continue + + if flag=='electrons' and len(line)>1: + numelec+=1 + ln=line.split() + ep=' '.join(ln[0:3]) + spin=ln[3] + radius=ln[4] + electrons[numelec]=[ep,spin,radius] + if numelec==1: + if emass!=0: massstr+="%d %s\n\n"%(types,emass) # electron mass=1 + else: massstr+="%d 1.000000\n\n"%(types) + continue + + if flag=='n_vels' and len(line)>1: + vels+=line+" 0.0" + continue + + if flag=='e_vels' and len(line)>1: + ln=line.split() + ln[0]=ln[0]+numnuclei + vels+=ln[0]+" "+ln[1]+" "+ln[2]+" "+ln[3]+" "+ln[4]+"\n" + continue + + if flag=='n_mass' and len(line)>1: + print "Setting nuclear masses is unsupported\n" + continue + + if flag=='e_mass' and len(line)>1: + print "Setting electron masses is unsupported\n" + continue + + print "\bDone" + + # Build data file + print "Writing datafile to %s ... "%('data.'+infile), + sys.stdout.flush() + print "\b"*19+"General section ", + 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)) + print "\b"*19+"Masses section ", + datafile.writelines(massstr) + print "\b"*19+"Atoms section ", + datafile.writelines("Atoms\n\n") + for n in range(numnuclei): + 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])) + for e in range(numelec): + 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])) + print "\b"*19+"Velocities section\n", + datafile.writelines(vels) + datafile.writelines("\n") + print "DONE .... GOODBYE !!" + datafile.close() + + # Build input script + import datetime + scriptfile.writelines(general%(datetime.date.today(),infile[:-4],boundary,cutoff,period)) + if op=='minimize': + scriptfile.writelines(minimize%('all',period,'all',period,steps,'10000')) + #%(group,period,group,period,iterations,fcalls) + elif op=='single_pt': + scriptfile.writelines(single_pt%()) + elif op=='dynamics': + if Tflag==True: + scriptfile.writelines(dynamics%('NVT',dt,ensemble['nvt']%('all',Tstart,Tstop,Tdamp,''),'all',period,'nvt','all',period,'nve',steps)) + #%(ensemble,dt,group,ensemble%(group,tstart,tstop,tdamp,options)) + else: + scriptfile.writelines(dynamics%('NVE',dt,ensemble['nve']%('all'),'all',period,'nve','all',period,'nve',steps)) + #%(ensemble,dt,group,ensemble%(group)) + scriptfile.writelines("\n") + +if __name__ == '__main__': + + # set defaults + + # check for input: + opts, argv = getopt(sys.argv[1:], 'h') + + # if no input, print help and exit + if len(argv) != 1: + printHelp() + sys.exit(1) + else: + infile=argv[0] + + # read options + for opt, arg in opts: + if opt == '-h': # -h: print help + printHelp() + + generate_lammps_input(infile) diff --git a/tools/eff/h2.out b/tools/eff/h2.out new file mode 100644 index 0000000000..2aaa9db9c8 --- /dev/null +++ b/tools/eff/h2.out @@ -0,0 +1,65 @@ + F0 F1 F2 F3 F4 F5 F6 F7 F8 F9 F10 F11 F12 F13 F14 F15 F16 F17 F18 F19 F20 F21 F22 F23 F24 F25 F26 F27 F28 F29 F30 F31 F32 F33 F34 F35 F36 F37 F38 F39 F40 F41 F42 F43 F44 F45 F46 F47 F48 F49 F50 F51 F52 F53 F54 F55 F56 F57 F58 F59 F60 F61 F62 F63 F64 F65 F66 F67 F68 F69 F70 F71 F72 F73 F74 F75 F76 F77 F78 F79 F80 F81 F82 F83 F84 F85 F86 F87 F88 F89 F90 F91 F92 F93 F94 F95 F96 F97 F98 F99 F100 +65 1.602500 1.847210 2.428450 2.854700 3.179100 4.544920 3.661700 3.154620 2.767460 3.478820 2.366160 3.155160 2.230730 2.352020 2.044080 2.049760 1.806560 1.864640 1.789170 1.712870 1.654070 1.661440 1.758570 1.867170 1.860790 2.005540 2.021950 2.223020 2.178060 2.676830 2.248710 1.893170 2.081190 1.902970 2.179950 2.205320 2.469800 3.079270 3.011320 3.192580 3.611520 3.535790 3.074110 2.845820 2.665760 2.622560 2.980290 3.278100 2.903910 2.963080 2.382150 2.458860 2.452530 2.353320 2.110870 1.764400 1.967500 1.750280 2.169140 2.531120 2.306520 2.463120 2.288620 2.304630 2.279590 2.696530 2.632870 2.908160 2.979250 2.721520 2.962370 2.850910 2.521280 2.819900 2.871190 2.765470 2.931630 2.822900 3.129440 2.460740 2.145160 2.092230 2.201780 2.231810 2.368860 2.226440 1.989590 1.670860 1.605980 1.639810 1.776830 2.192250 2.005160 1.971960 2.017060 1.910040 1.856710 1.925730 1.773370 1.625320 1.723740 +66 1.602500 1.543820 1.746750 1.767360 1.990970 2.019260 1.909180 1.819990 1.627490 1.734930 1.641380 1.646010 1.896660 2.014890 2.144340 2.379700 2.395860 2.403360 2.434960 2.576080 2.086380 1.804740 1.800590 1.719790 1.740230 1.768660 1.917620 1.984760 1.942770 2.937550 3.075790 2.438570 3.216960 2.554580 2.378440 2.391660 2.552000 2.253090 2.572630 2.107210 2.765400 2.835970 2.942400 2.881330 2.885680 2.988990 3.142540 2.925960 2.986040 2.736770 2.797410 2.745800 3.545530 2.992570 2.698270 2.468860 2.495980 2.768810 2.908330 3.097850 2.748750 2.922960 2.520550 2.763420 2.728250 2.596690 3.222620 2.727130 3.607610 3.545550 3.430170 3.362950 3.502410 3.214580 2.807740 3.168070 2.968940 3.146240 2.502160 3.214370 2.511880 2.457440 2.682270 2.759590 2.743480 2.873990 2.896230 2.909750 2.904970 3.362240 3.686490 3.516310 3.563890 3.690950 3.166930 3.262190 2.951360 2.694090 3.445350 2.861470 2.849300 +67 1.602500 1.531100 1.586730 2.014180 2.195620 2.007930 1.960860 2.217590 1.794480 1.698470 1.938620 1.791000 1.983490 2.077880 2.007480 2.328330 2.080550 2.029670 2.011440 1.770340 1.931580 1.811050 1.938320 2.752640 2.003110 2.083280 2.184880 2.705970 2.691800 2.918750 3.247420 3.493530 2.879350 2.848360 2.946620 3.161330 2.809910 2.940800 2.818490 2.799750 2.718940 2.795540 2.639180 2.771040 2.739290 3.059810 2.710810 2.748410 3.178220 2.565960 2.589490 2.903570 2.590920 2.957380 2.536220 2.727300 2.939390 3.079050 3.154390 2.318730 3.019290 2.804410 3.162520 2.929660 2.752950 2.519810 2.740460 2.731370 3.336120 3.158610 3.351360 2.967940 2.728890 2.985110 3.149860 2.988220 2.862160 3.070600 3.099590 2.812730 2.896110 3.057120 3.007410 2.830630 3.473040 3.286630 3.371790 3.437820 3.023400 3.044100 3.557510 3.135460 3.472420 3.425260 2.984170 2.986280 2.837600 3.516970 2.987890 2.953560 3.327330 +68 1.602500 1.823270 1.726220 2.027900 1.955060 1.889310 1.973570 1.828170 1.827770 1.832220 2.151660 2.147630 2.082060 2.186460 2.588260 2.331100 2.165690 2.103310 1.945430 1.847610 1.591490 1.664170 1.717660 1.643040 1.750960 1.974050 2.098720 2.449810 2.278370 2.527890 2.858990 2.558740 3.726120 2.909590 3.412140 3.635960 3.581880 2.988360 2.972220 2.282060 2.853520 2.446860 2.524670 1.952800 2.076430 2.053950 2.006230 1.800470 1.709250 1.975390 1.793320 1.709900 2.039730 2.192860 2.978840 2.626290 3.197820 3.139000 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3.187780 3.224180 2.628190 2.509690 2.863070 2.768950 2.439560 2.764370 2.418220 2.630720 2.480110 2.101440 2.323280 2.186500 2.159890 2.241330 2.257090 2.649870 2.768700 3.272990 2.885520 2.526190 3.467720 3.578330 3.337000 3.094180 2.959720 2.826810 2.731410 3.078140 2.948790 3.360180 3.038270 2.851860 2.818550 3.560670 3.372410 3.058940 3.333360 2.907520 2.763580 3.332730 2.568430 2.835660 3.365710 2.851620 2.930880 2.550820 2.545050 2.687890 2.738240 2.403390 2.806410 diff --git a/tools/eff/h2.vmd b/tools/eff/h2.vmd new file mode 100644 index 0000000000..4dd5f834ca --- /dev/null +++ b/tools/eff/h2.vmd @@ -0,0 +1,215 @@ +# module radii.vmd +# December, 2009 -(c)- Andres Jaramillo-Botero +# Script to load variable changing radii onto a pEFF lammpstrj file + +# radii.vmd -- +# Script to read and change electron radii in vmd dynamics traj +# + +# openFile -- +# Open the file and start looking for data +# +# Arguments: +# filename Name of the file to read +# +# Result: +# infile Handle to the opened file +# +# Side effects: +# A file in question is opened. Lines containing a * or# as +# the first non-blank character are considered comments. The +# first line without this is considered to be a line with the +# names of the columns. +# +proc openFile {filename} { + set infile [open $filename "r"] + return $infile +} + +# readNames -- +# Read the names of the columns +# +# Arguments: +# infile Handle to the file +# +# Result: +# names List of names, the number indicates the number of +# the snapshot frame +# +proc readNames {infile} { + # + # Skip the header - if any + # + set pos 0 + while { [gets $infile line] >= 0 } { + if { [regexp {[ \t]*[*#]} $line] } { + incr pos + } else { + break + } + } + seek $infile 0 start + while { $pos > 0 } { + gets $infile line + incr pos -1 + } + + # + # Read the line with the column names + # + gets $infile line + + # Force the line to be interpreted as a list + set nocols [llength $line] + + return $line +} + +# readData -- +# Read the data per line +# +# Arguments: +# infile Handle to the file +# +# Result: +# values List of values, representing each column. +# A list of length zero indicates the end of file +# +proc readData {infile} { + while { [gets $infile values] == 0 } { ;# Just go on - skip empty lines } + + set nocols [llength $values] + + return $values +} + +# readFile -- +# Read the file and store the data in a (global) array +# +# Arguments: +# filename Name of the file +# +# Result: +# None +# +# Side effects: +# Filled array, ready for display +# +proc readFile {filename} { + global data_array + + set infile [openFile $filename] + + set data_array(names) [readNames $infile] + set i 0 + foreach name $data_array(names) { + set data_array($i) {} + incr i + } + + while 1 { + set values [readData $infile] + if { [llength $values] > 0 } { + set i 0 + foreach value $values { + lappend data_array($i) $value + incr i + } + } else { + break + } + } +} + +# makeXYData -- +# Make a list useable by frame-electron +# +# Arguments: +# xindex Index of frame data +# yindex Index of electron data +# +# Result: +# None +# +# Side effects: +# A dataset for changing the electron radii, per trajectory frame +# +proc makeXYData {xindex yindex} { + global data_array + + set xydata {} + foreach x $data_array($xindex) y $data_array($yindex) { + lappend xydata $x $y + } + return $xydata +} + +proc returnXYPair {x y} { + global data_array + + return [list $data_array($x) $data_array($y)] +} + +# do_radii -- +# Changes the radii of electrons per trajectory frame +# +# Arguments: +# xindex Index of frame data +# yindex Index of electron data +# +# Result: +# prints the frame:atomID:radius +# +proc do_radii {args} { + global molid data_array + + #set n [molinfo $molid get numatoms] + set f [molinfo $molid get frame] + + set fr [expr {$f+1}] + + 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 + $s set radius $nr + $s delete + #puts stderr "$fr $elec $nr" + } +} + +# main -- +# Main control flow +# + +# Check input arguments +#for {set i 0} {$i<[llength $argv]} {incr i} +# puts " - $i: [lindex $argv $i]" + +global data_array molid + +# Set input files manually +set xyz h2.xyz +set data h2.out + +# switch default rep to VDW. +mol default style VDW + +# load nuclear and electron xyz trajectory +#set xyz [lindex $::argv 0] + +# load electron radii information for trajectory +#set datafile [lindex $::argv 1] + +set molid [mol new $xyz waitfor all] +mol modstyle 0 [molinfo top] VDW 1.0 32.0 + +puts "Starting ..." +readFile $data +puts "Read datafile and created array of radii ..." + +puts "Visualize trajectory" +trace variable vmd_frame($molid) w do_radii +animate goto start +do_radii + diff --git a/tools/eff/h2.xyz b/tools/eff/h2.xyz new file mode 100644 index 0000000000..2a7c6a0c88 --- /dev/null +++ b/tools/eff/h2.xyz @@ -0,0 +1,13130 @@ +128 +Atoms +1 1.6120 1.6120 2.5752 +1 1.6120 1.6120 3.8728 +1 1.6120 1.6120 9.0231 +1 1.6120 1.6120 10.3208 +1 1.6120 4.8360 2.5752 +1 1.6120 4.8360 3.8728 +1 1.6120 4.8360 9.0231 +1 1.6120 4.8360 10.3208 +1 1.6120 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-0.1987 1.4601 +2 8.7368 1.7921 11.0627 +2 9.2028 5.2850 9.1053 +2 12.6930 10.9631 7.1856 +2 0.5523 7.9593 0.0464 +2 9.6607 0.3871 7.0055 +2 6.9612 10.2956 7.9719 +2 4.8575 6.3651 10.0546 +2 11.1003 10.8883 10.6208 +2 7.9596 2.6946 3.9506 +2 12.6944 2.2222 9.1303 +2 11.4896 10.0485 2.8853 +2 0.9410 6.6313 4.0996 +2 3.8004 1.4878 11.6597 +2 3.1862 0.1274 7.1361 diff --git a/tools/eff/lmp2data.py b/tools/eff/lmp2data.py new file mode 100644 index 0000000000..532fa55d5f --- /dev/null +++ b/tools/eff/lmp2data.py @@ -0,0 +1,144 @@ +#!/usr/local/bin/python-2.5/bin/python + +Info=""" +Module name: lmp2data.py + +Author: (c) Andres Jaramillo-Botero +California Institute of Technology +ajaramil@wag.caltech.edu +Project: pEFF +Version: August 2009 + +Extracts the electron radii from a lammps trajectory dump of style custom: + +dump 1 all custom period dump_file id type x y z spin radius ... + +NOTE: The radius must be the i'th column per trajectory entry in the dump file + +""" + +# import essentials: +import sys, os +from math import log10 +from shutil import rmtree +from getopt import gnu_getopt as getopt +import numpy + +def printHelp(): + print Info + print "Usage: python lmp2data.py test.lammpstrj\n" + return + +def makeradii(infile,outfile,column,flag_all): + + print "Reading %s ... [WAIT]"%infile, + fin = open(infile,'r') + lines = fin.xreadlines() + print 7*"\b"+"[DONE]" + frame=0 + radii=[] + # grep the number of frames and atoms/frame + os.system("grep TIMESTEP %s | wc -l > frames; grep -m 1 -A 1 ATOMS %s > atoms; grep -m 1 \"ITEM: ATOMS\" %s > params"%(infile,infile,infile)) + tmp=open("frames",'r') + frames=int(tmp.readline().split()[0]) + tmp.close() + tmp=open("atoms",'r') + atoms=int(tmp.readlines()[1].split()[0]) + tmp.close() + tmp=open("params",'r') + ids=tmp.readline().split()[2:] + os.system("rm -rf frames atoms params") + arry=numpy.zeros((atoms,frames),dtype=str) + framecnt=0 + header=9 + ecount=0 + if flag_all==True: atom_type="nuclei and electron" + else: atom_type="electron" + print "Extracting %s %s per frame from %s ... "%(atom_type,ids[column],infile), + for i,line in enumerate(lines): + lo=(atoms+header)*framecnt+header + hi=lo+atoms + if (i= lo) and (i < hi): + lparse=line.split() + id=int(lparse[0]) +# r=float(lparse[column-1]) + r=lparse[column] +# if (float(r)!=0): + arry[id-1][framecnt]=r + print arry[id-1][framecnt],r,raw_input() + if (float(r)!=0) and (framecnt==0): ecount+=1 +# else: arry[id-1][framecnt]=r + if (i==lo+1): + sys.stdout.write("%d/%d%s"%(framecnt+1,frames,(int(log10(framecnt+1))+3+int(log10(frames)))*"\b")) + sys.stdout.flush() + if (i == hi+1): + framecnt+=1 + + print + if outfile=="": + outfile=infile+'.%s'%(ids[column]) + fout=open(outfile,'w') + else: fout=open(outfile,'w') + print "Writing %s/frame table to %s ... "%(ids[column],outfile), + sys.stdout.flush() + + for i in range(frames): + fout.writelines('\tF'+str(i)) + fout.writelines("\n") + e=1 + for a in range(atoms): + if flag_all==True: + sys.stdout.write("%d/%d%s"%(a+1,atoms,(int(log10(a+1))+int(log10(atoms))+3)*"\b")) + sys.stdout.flush() + fout.writelines("%d\t"%(a+1)) + for f in range(frames): + fout.writelines("%s\t"%(arry[a][f])) + fout.writelines("\n") + else: + if arry[a][0] == 0.0: + continue + else: + sys.stdout.write("%d/%d%s"%(e,ecount,(int(log10(e))+int(log10(ecount))+3)*"\b")) + sys.stdout.flush() + e+=1 + fout.writelines("%d\t"%(a+1)) + for f in range(frames): + fout.writelines("%s\t"%(arry[a][f])) + fout.writelines("\n") + + print + print "DONE .... GOODBYE !!" + fout.close() + fin.close() + +if __name__ == '__main__': + + # set defaults + outfile = "" + flag_all = False + column=6 # default = radius + + # check for input: + opts, argv = getopt(sys.argv[1:], 'c:o:ha') + + # if no input, print help and exit + if len(argv) != 1: + printHelp() + sys.exit(1) + else: + infile=argv[0] + + # read options + for opt, arg in opts: + if opt == '-h': # -h: print help + printHelp() + if opt == '-o': # output file name + outfile=arg + if opt == '-a': # all nuclii+electrons + flag_all=True + if opt == '-c': # select column from lammpstrj file to tabulate + column=int(arg) + + makeradii(infile,outfile,column,flag_all) diff --git a/tools/eff/lmp2radii.c b/tools/eff/lmp2radii.c new file mode 100644 index 0000000000..b62da070ba --- /dev/null +++ b/tools/eff/lmp2radii.c @@ -0,0 +1,2588 @@ +/* Generated by Cython 0.9.8.1.1 on Thu Oct 1 16:33:24 2009 */ + +#define PY_SSIZE_T_CLEAN +#include "Python.h" +#include "structmember.h" +#ifndef PY_LONG_LONG + #define PY_LONG_LONG LONG_LONG +#endif +#ifndef DL_EXPORT + #define DL_EXPORT(t) t +#endif +#if PY_VERSION_HEX < 0x02040000 + #define METH_COEXIST 0 +#endif +#if PY_VERSION_HEX < 0x02050000 + typedef int Py_ssize_t; + #define PY_SSIZE_T_MAX INT_MAX + #define PY_SSIZE_T_MIN INT_MIN + #define PyInt_FromSsize_t(z) PyInt_FromLong(z) + #define PyInt_AsSsize_t(o) PyInt_AsLong(o) + #define PyNumber_Index(o) PyNumber_Int(o) + #define PyIndex_Check(o) PyNumber_Check(o) +#endif +#if PY_VERSION_HEX < 0x02060000 + #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) + #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type) + #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size) + #define PyVarObject_HEAD_INIT(type, size) \ + PyObject_HEAD_INIT(type) size, + #define PyType_Modified(t) + + typedef struct { + void *buf; + Py_ssize_t len; + int readonly; + const char *format; + int ndim; + Py_ssize_t *shape; + Py_ssize_t *strides; + Py_ssize_t *suboffsets; + Py_ssize_t itemsize; + void *internal; + } Py_buffer; + + #define PyBUF_SIMPLE 0 + #define PyBUF_WRITABLE 0x0001 + #define PyBUF_LOCK 0x0002 + #define PyBUF_FORMAT 0x0004 + #define PyBUF_ND 0x0008 + #define PyBUF_STRIDES (0x0010 | PyBUF_ND) + #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES) + #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES) + #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES) + #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES) + +#endif +#if PY_MAJOR_VERSION < 3 + #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" +#else + #define __Pyx_BUILTIN_MODULE_NAME "builtins" +#endif +#if PY_MAJOR_VERSION >= 3 + #define Py_TPFLAGS_CHECKTYPES 0 + #define Py_TPFLAGS_HAVE_INDEX 0 +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBaseString_Type PyUnicode_Type + #define PyString_Type PyBytes_Type + #define PyInt_Type PyLong_Type + #define PyInt_Check(op) PyLong_Check(op) + #define PyInt_CheckExact(op) PyLong_CheckExact(op) + #define PyInt_FromString PyLong_FromString + #define PyInt_FromUnicode PyLong_FromUnicode + #define PyInt_FromLong PyLong_FromLong + #define PyInt_FromSize_t PyLong_FromSize_t + #define PyInt_FromSsize_t PyLong_FromSsize_t + #define PyInt_AsLong PyLong_AsLong + #define PyInt_AS_LONG PyLong_AS_LONG + #define PyInt_AsSsize_t PyLong_AsSsize_t + #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask + #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask + #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) +#else + #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) + #define PyBytes_Type PyString_Type +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyMethod_New(func, self, klass) PyInstanceMethod_New(func) +#endif +#if !defined(WIN32) && !defined(MS_WINDOWS) + #ifndef __stdcall + #define __stdcall + #endif + #ifndef __cdecl + #define __cdecl + #endif +#else + #define _USE_MATH_DEFINES +#endif +#ifdef __cplusplus +#define __PYX_EXTERN_C extern "C" +#else +#define __PYX_EXTERN_C extern +#endif +#include +#define __PYX_HAVE_API__lmp2radii + + +#ifdef __GNUC__ +#define INLINE __inline__ +#elif _WIN32 +#define INLINE __inline +#else +#define INLINE +#endif + +typedef struct {PyObject **p; char *s; long n; char is_unicode; char intern; char is_identifier;} __Pyx_StringTabEntry; /*proto*/ + + + +static int __pyx_skip_dispatch = 0; + + +/* Type Conversion Predeclarations */ + +#if PY_MAJOR_VERSION < 3 +#define __Pyx_PyBytes_FromString PyString_FromString +#define __Pyx_PyBytes_AsString PyString_AsString +#else +#define __Pyx_PyBytes_FromString PyBytes_FromString +#define __Pyx_PyBytes_AsString PyBytes_AsString +#endif + +#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) +static INLINE int __Pyx_PyObject_IsTrue(PyObject* x); +static INLINE PY_LONG_LONG __pyx_PyInt_AsLongLong(PyObject* x); +static INLINE unsigned PY_LONG_LONG __pyx_PyInt_AsUnsignedLongLong(PyObject* x); +static INLINE Py_ssize_t __pyx_PyIndex_AsSsize_t(PyObject* b); + +#define __pyx_PyInt_AsLong(x) (PyInt_CheckExact(x) ? PyInt_AS_LONG(x) : PyInt_AsLong(x)) +#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) + +static INLINE unsigned char __pyx_PyInt_unsigned_char(PyObject* x); +static INLINE unsigned short __pyx_PyInt_unsigned_short(PyObject* x); +static INLINE char __pyx_PyInt_char(PyObject* x); +static INLINE short __pyx_PyInt_short(PyObject* x); +static INLINE int __pyx_PyInt_int(PyObject* x); +static INLINE long __pyx_PyInt_long(PyObject* x); +static INLINE signed char __pyx_PyInt_signed_char(PyObject* x); +static INLINE signed short __pyx_PyInt_signed_short(PyObject* x); +static INLINE signed int __pyx_PyInt_signed_int(PyObject* x); +static INLINE signed long __pyx_PyInt_signed_long(PyObject* x); +static INLINE long double __pyx_PyInt_long_double(PyObject* x); +#ifdef __GNUC__ +/* Test for GCC > 2.95 */ +#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) +#define likely(x) __builtin_expect(!!(x), 1) +#define unlikely(x) __builtin_expect(!!(x), 0) +#else /* __GNUC__ > 2 ... */ +#define likely(x) (x) +#define unlikely(x) (x) +#endif /* __GNUC__ > 2 ... */ +#else /* __GNUC__ */ +#define likely(x) (x) +#define unlikely(x) (x) +#endif /* __GNUC__ */ + +static PyObject *__pyx_m; +static PyObject *__pyx_b; +static PyObject *__pyx_empty_tuple; +static int __pyx_lineno; +static int __pyx_clineno = 0; +static const char * __pyx_cfilenm= __FILE__; +static const char *__pyx_filename; +static const char **__pyx_f; + +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/ + +static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/ + +static PyObject *__Pyx_UnpackItem(PyObject *, Py_ssize_t index); /*proto*/ +static int __Pyx_EndUnpack(PyObject *); /*proto*/ + +static INLINE PyObject *__Pyx_GetItemInt(PyObject *o, Py_ssize_t i, int is_unsigned) { + PyObject *r; + if (PyList_CheckExact(o) && 0 <= i && i < PyList_GET_SIZE(o)) { + r = PyList_GET_ITEM(o, i); + Py_INCREF(r); + } + else if (PyTuple_CheckExact(o) && 0 <= i && i < PyTuple_GET_SIZE(o)) { + r = PyTuple_GET_ITEM(o, i); + Py_INCREF(r); + } + else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0) || !is_unsigned)) + r = PySequence_GetItem(o, i); + else { + PyObject *j = (likely(i >= 0) || !is_unsigned) ? PyInt_FromLong(i) : PyLong_FromUnsignedLongLong((sizeof(unsigned long long) > sizeof(Py_ssize_t) ? (1ULL << (sizeof(Py_ssize_t)*8)) : 0) + i); + if (!j) + return 0; + r = PyObject_GetItem(o, j); + Py_DECREF(j); + } + return r; +} + +static int __Pyx_Print(PyObject *, int); /*proto*/ +#if PY_MAJOR_VERSION >= 3 +static PyObject* __pyx_print = 0; +static PyObject* __pyx_print_kwargs = 0; +#endif + +static void __Pyx_AddTraceback(const char *funcname); /*proto*/ + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ + +/* Type declarations */ +/* Module declarations from lmp2radii */ + + + +/* Implementation of lmp2radii */ +static char __pyx_k_1[] = "\nModule name: lmp2radii.py \n\nAuthor: (c) Andres Jaramillo-Botero\nCalifornia Institute of Technology\najaramil@wag.caltech.edu\nProject: pEFF\nVersion: August 2009\n\nExtracts the electron radii from a lammps trajectory dump of style custom:\n\ndump 1 all custom period dump_file id type x y z spin radius ...\n\nNOTE: The radius must be the 6th column per trajectory entry in the dump file\n\n"; +static char __pyx_k_5[] = "-h"; +static PyObject *__pyx_int_1; +static PyObject *__pyx_int_7; +static PyObject *__pyx_int_0; +static PyObject *__pyx_int_9; +static PyObject *__pyx_int_3; +static char __pyx_k_Info[] = "Info"; +static PyObject *__pyx_kp_Info; +static char __pyx_k_sys[] = "sys"; +static PyObject *__pyx_kp_sys; +static char __pyx_k_os[] = "os"; +static PyObject *__pyx_kp_os; +static char __pyx_k_math[] = "math"; +static PyObject *__pyx_kp_math; +static char __pyx_k_2[] = "log10"; +static PyObject *__pyx_kp_2; +static char __pyx_k_shutil[] = "shutil"; +static PyObject *__pyx_kp_shutil; +static char __pyx_k_rmtree[] = "rmtree"; +static PyObject *__pyx_kp_rmtree; +static char __pyx_k_getopt[] = "getopt"; +static PyObject *__pyx_kp_getopt; +static char __pyx_k_gnu_getopt[] = "gnu_getopt"; +static PyObject *__pyx_kp_gnu_getopt; +static char __pyx_k_numpy[] = "numpy"; +static PyObject *__pyx_kp_numpy; +static char __pyx_k___name__[] = "__name__"; +static PyObject *__pyx_kp___name__; +static char __pyx_k_3[] = "__main__"; +static PyObject *__pyx_kp_3; +static char __pyx_k_argv[] = "argv"; +static PyObject *__pyx_kp_argv; +static char __pyx_k_4[] = "h"; +static PyObject *__pyx_kp_4; +static char __pyx_k_opts[] = "opts"; +static PyObject *__pyx_kp_opts; +static char __pyx_k_printHelp[] = "printHelp"; +static PyObject *__pyx_kp_printHelp; +static char __pyx_k_exit[] = "exit"; +static PyObject *__pyx_kp_exit; +static char __pyx_k_infile[] = "infile"; +static PyObject *__pyx_kp_infile; +static char __pyx_k_opt[] = "opt"; +static PyObject *__pyx_kp_opt; +static char __pyx_k_arg[] = "arg"; +static PyObject *__pyx_kp_arg; +static char __pyx_k_makeradii[] = "makeradii"; +static PyObject *__pyx_kp_makeradii; +static char __pyx_k_open[] = "open"; +static PyObject *__pyx_kp_open; +static char __pyx_k_8[] = "r"; +static PyObject *__pyx_kp_8; +static char __pyx_k_xreadlines[] = "xreadlines"; +static PyObject *__pyx_kp_xreadlines; +static char __pyx_k_system[] = "system"; +static PyObject *__pyx_kp_system; +static char __pyx_k_12[] = "frames"; +static PyObject *__pyx_kp_12; +static char __pyx_k_13[] = "r"; +static PyObject *__pyx_kp_13; +static char __pyx_k_readline[] = "readline"; +static PyObject *__pyx_kp_readline; +static char __pyx_k_split[] = "split"; +static PyObject *__pyx_kp_split; +static char __pyx_k_close[] = "close"; +static PyObject *__pyx_kp_close; +static char __pyx_k_14[] = "atoms"; +static PyObject *__pyx_kp_14; +static char __pyx_k_15[] = "r"; +static PyObject *__pyx_kp_15; +static char __pyx_k_readlines[] = "readlines"; +static PyObject *__pyx_kp_readlines; +static char __pyx_k_zeros[] = "zeros"; +static PyObject *__pyx_kp_zeros; +static char __pyx_k_dtype[] = "dtype"; +static PyObject *__pyx_kp_dtype; +static char __pyx_k_enumerate[] = "enumerate"; +static PyObject *__pyx_kp_enumerate; +static char __pyx_k_stdout[] = "stdout"; +static PyObject *__pyx_kp_stdout; +static char __pyx_k_write[] = "write"; +static PyObject *__pyx_kp_write; +static char __pyx_k_flush[] = "flush"; +static PyObject *__pyx_kp_flush; 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[WAIT]"; +static char __pyx_k_9[] = ""; +static char __pyx_k_10[] = "[DONE]"; +static char __pyx_k_11[] = "grep TIMESTEP %s | wc -l > frames; grep -m 1 -A 1 ATOMS %s > atoms"; +static char __pyx_k_16[] = "rm -rf frames atoms"; +static char __pyx_k_17[] = "Extracting electron radii per frame from %s ... "; +static char __pyx_k_18[] = "%d/%d%s"; +static char __pyx_k_19[] = ""; +static char __pyx_k_20[] = "Writing radii/frame table to %s ... "; +static char __pyx_k_21[] = ".out"; +static char __pyx_k_22[] = ".out"; +static char __pyx_k_24[] = "\tF"; +static char __pyx_k_25[] = "\n"; +static char __pyx_k_26[] = "%d/%d%s"; +static char __pyx_k_27[] = ""; +static char __pyx_k_28[] = "%d\t"; +static char __pyx_k_29[] = "%f\t"; +static char __pyx_k_30[] = "\n"; +static char __pyx_k_31[] = "DONE .... 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+} + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + while (t->p) { + #if PY_MAJOR_VERSION < 3 + if (t->is_unicode && (!t->is_identifier)) { + *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); + } else if (t->intern) { + *t->p = PyString_InternFromString(t->s); + } else { + *t->p = PyString_FromStringAndSize(t->s, t->n - 1); + } + #else /* Python 3+ has unicode identifiers */ + if (t->is_identifier || (t->is_unicode && t->intern)) { + *t->p = PyUnicode_InternFromString(t->s); + } else if (t->is_unicode) { + *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); + } else { + *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); + } + #endif + if (!*t->p) + return -1; + ++t; + } + return 0; +} + +/* Type Conversion Functions */ + +static INLINE Py_ssize_t __pyx_PyIndex_AsSsize_t(PyObject* b) { + Py_ssize_t ival; + PyObject* x = PyNumber_Index(b); + if (!x) return -1; + ival = PyInt_AsSsize_t(x); + Py_DECREF(x); + return ival; +} + +static INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { + if (x == Py_True) return 1; + else if (x == Py_False) return 0; + else return PyObject_IsTrue(x); +} + +static INLINE PY_LONG_LONG __pyx_PyInt_AsLongLong(PyObject* x) { + if (PyInt_CheckExact(x)) { + return PyInt_AS_LONG(x); + } + else if (PyLong_CheckExact(x)) { + return PyLong_AsLongLong(x); + } + else { + PY_LONG_LONG val; + PyObject* tmp = PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; + val = __pyx_PyInt_AsLongLong(tmp); + Py_DECREF(tmp); + return val; + } +} + +static INLINE unsigned PY_LONG_LONG __pyx_PyInt_AsUnsignedLongLong(PyObject* x) { + if (PyInt_CheckExact(x)) { + long val = PyInt_AS_LONG(x); + if (unlikely(val < 0)) { + PyErr_SetString(PyExc_TypeError, "Negative assignment to unsigned type."); + return (unsigned PY_LONG_LONG)-1; + } + return val; + } + else if (PyLong_CheckExact(x)) { + return PyLong_AsUnsignedLongLong(x); + } + else { + PY_LONG_LONG val; + PyObject* tmp = PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; + val = __pyx_PyInt_AsUnsignedLongLong(tmp); + Py_DECREF(tmp); + return val; + } +} + + +static INLINE unsigned char __pyx_PyInt_unsigned_char(PyObject* x) { + if (sizeof(unsigned char) < sizeof(long)) { + long long_val = __pyx_PyInt_AsLong(x); + unsigned char val = (unsigned char)long_val; + if (unlikely((val != long_val) || (long_val < 0))) { + PyErr_SetString(PyExc_OverflowError, "value too large to convert to unsigned char"); + return (unsigned char)-1; + } + return val; + } + else { + return __pyx_PyInt_AsLong(x); + } +} + +static INLINE unsigned short __pyx_PyInt_unsigned_short(PyObject* x) { + if (sizeof(unsigned short) < sizeof(long)) { + long long_val = __pyx_PyInt_AsLong(x); + unsigned short val = (unsigned short)long_val; + if (unlikely((val != long_val) || (long_val < 0))) { + PyErr_SetString(PyExc_OverflowError, "value too large to convert to unsigned short"); + return (unsigned short)-1; + } + return val; + } + else { + return __pyx_PyInt_AsLong(x); + } +} + +static INLINE char __pyx_PyInt_char(PyObject* x) { + if (sizeof(char) < sizeof(long)) { + long long_val = __pyx_PyInt_AsLong(x); + char val = (char)long_val; + if (unlikely((val != long_val) )) { + PyErr_SetString(PyExc_OverflowError, "value too large to convert to char"); + return (char)-1; + } + return val; + } + else { + return __pyx_PyInt_AsLong(x); + } +} + +static INLINE short __pyx_PyInt_short(PyObject* x) { + if (sizeof(short) < sizeof(long)) { + long long_val = __pyx_PyInt_AsLong(x); + short val = (short)long_val; + if (unlikely((val != long_val) )) { + PyErr_SetString(PyExc_OverflowError, "value too large to convert to short"); + return (short)-1; + } + return val; + } + else { + return __pyx_PyInt_AsLong(x); + } +} + +static INLINE int __pyx_PyInt_int(PyObject* x) { + if (sizeof(int) < sizeof(long)) { + long long_val = __pyx_PyInt_AsLong(x); + int val = (int)long_val; + if (unlikely((val != long_val) )) { + PyErr_SetString(PyExc_OverflowError, "value too large to convert to int"); + return (int)-1; + } + return val; + } + else { + return __pyx_PyInt_AsLong(x); + } +} + +static INLINE long __pyx_PyInt_long(PyObject* x) { + if (sizeof(long) < sizeof(long)) { + long long_val = __pyx_PyInt_AsLong(x); + long val = (long)long_val; + if (unlikely((val != long_val) )) { + PyErr_SetString(PyExc_OverflowError, "value too large to convert to long"); + return (long)-1; + } + return val; + } + else { + return __pyx_PyInt_AsLong(x); + } +} + +static INLINE signed char __pyx_PyInt_signed_char(PyObject* x) { + if (sizeof(signed char) < sizeof(long)) { + long long_val = __pyx_PyInt_AsLong(x); + signed char val = (signed char)long_val; + if (unlikely((val != long_val) )) { + PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed char"); + return (signed char)-1; + } + return val; + } + else { + return __pyx_PyInt_AsLong(x); + } +} + +static INLINE signed short __pyx_PyInt_signed_short(PyObject* x) { + if (sizeof(signed short) < sizeof(long)) { + long long_val = __pyx_PyInt_AsLong(x); + signed short val = (signed short)long_val; + if (unlikely((val != long_val) )) { + PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed short"); + return (signed short)-1; + } + return val; + } + else { + return __pyx_PyInt_AsLong(x); + } +} + +static INLINE signed int __pyx_PyInt_signed_int(PyObject* x) { + if (sizeof(signed int) < sizeof(long)) { + long long_val = __pyx_PyInt_AsLong(x); + signed int val = (signed int)long_val; + if (unlikely((val != long_val) )) { + PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed int"); + return (signed int)-1; + } + return val; + } + else { + return __pyx_PyInt_AsLong(x); + } +} + +static INLINE signed long __pyx_PyInt_signed_long(PyObject* x) { + if (sizeof(signed long) < sizeof(long)) { + long long_val = __pyx_PyInt_AsLong(x); + signed long val = (signed long)long_val; + if (unlikely((val != long_val) )) { + PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed long"); + return (signed long)-1; + } + return val; + } + else { + return __pyx_PyInt_AsLong(x); + } +} + +static INLINE long double __pyx_PyInt_long_double(PyObject* x) { + if (sizeof(long double) < sizeof(long)) { + long long_val = __pyx_PyInt_AsLong(x); + long double val = (long double)long_val; + if (unlikely((val != long_val) )) { + PyErr_SetString(PyExc_OverflowError, "value too large to convert to long double"); + return (long double)-1; + } + return val; + } + else { + return __pyx_PyInt_AsLong(x); + } +} + diff --git a/tools/eff/lmp2radii.py b/tools/eff/lmp2radii.py new file mode 100644 index 0000000000..28c23d6289 --- /dev/null +++ b/tools/eff/lmp2radii.py @@ -0,0 +1,113 @@ +#!/usr/local/bin/python-2.5/bin/python + +Info=""" +Module name: lmp2radii.py + +Author: (c) Andres Jaramillo-Botero +California Institute of Technology +ajaramil@wag.caltech.edu +Project: pEFF +Version: August 2009 + +Extracts the electron radii from a lammps trajectory dump of style custom: + +dump 1 all custom period dump_file id type x y z spin radius ... + +NOTE: The radius must be the 6th column per trajectory entry in the dump file + +""" + +# import essentials: +import sys, os +from math import log10 +from shutil import rmtree +from getopt import gnu_getopt as getopt +import numpy + +def printHelp(): + print Info + print "Usage: python lmp2radii.pyx test.lammpstrj\n" + return + +def makeradii(infile): + + print "Reading %s ... [WAIT]"%infile, + fin = open(infile,'r') + lines = fin.xreadlines() + print 7*"\b"+"[DONE]" + frame=0 + radii=[] + # grep the number of frames and atoms/frame + os.system("grep TIMESTEP %s | wc -l > frames; grep -m 1 -A 1 ATOMS %s > atoms"%(infile,infile)) + tmp=open("frames",'r') + frames=int(tmp.readline().split()[0]) + tmp.close() + tmp=open("atoms",'r') + atoms=int(tmp.readlines()[1].split()[0]) + tmp.close() + os.system("rm -rf frames atoms") + arry=numpy.zeros((atoms,frames),dtype=float) + framecnt=0 + header=9 + ecount=0 + print "Extracting electron radii per frame from %s ... "%(infile), + for i,line in enumerate(lines): + lo=(atoms+header)*framecnt+header + hi=lo+atoms + if (i= lo) and (i < hi): + lparse=line.split() + id=int(lparse[0]) + r=float(lparse[6]) + if (r!=0): + arry[id-1][framecnt]=r + if (framecnt==0): ecount+=1 + if (i==lo+1): + sys.stdout.write("%d/%d%s"%(framecnt+1,frames,(int(log10(framecnt+1))+3+int(log10(frames)))*"\b")) + sys.stdout.flush() + if (i == hi+1): + framecnt+=1 + print + print "Writing radii/frame table to %s ... "%(infile+'.out'), + sys.stdout.flush() + fout=open(infile+'.out','w') + for i in range(frames): + fout.writelines('\tF'+str(i)) + fout.writelines("\n") + e=1 + for a in range(atoms): + if arry[a][0] == 0.0: continue + else: + sys.stdout.write("%d/%d%s"%(e,ecount,(int(log10(e))+int(log10(ecount))+3)*"\b")) + sys.stdout.flush() + e+=1 + fout.writelines("%d\t"%(a+1)) + for f in range(frames): + fout.writelines("%f\t"%(arry[a][f])) + fout.writelines("\n") + print + print "Done !! (generated radii/frame table) \n" + fout.close() + fin.close() + +if __name__ == '__main__': + + # set defaults + + # check for input: + opts, argv = getopt(sys.argv[1:], 'h') + + # if no input, print help and exit + if len(argv) != 1: + printHelp() + sys.exit(1) + else: + infile=argv[0] + + # read options + for opt, arg in opts: + if opt == '-h': # -h: print help + printHelp() + + makeradii(infile) diff --git a/tools/eff/lmp2radii.pyx b/tools/eff/lmp2radii.pyx new file mode 100644 index 0000000000..f114f243ca --- /dev/null +++ b/tools/eff/lmp2radii.pyx @@ -0,0 +1,113 @@ +#!/usr/local/bin/python-2.5/bin/python + +Info=""" +Module name: lmp2radii.py + +Author: (c) Andres Jaramillo-Botero +California Institute of Technology +ajaramil@wag.caltech.edu +Project: pEFF +Version: August 2009 + +Extracts the electron radii from a lammps trajectory dump of style custom: + +dump 1 all custom period dump_file id type x y z spin radius ... + +NOTE: The radius must be the 6th column per trajectory entry in the dump file + +""" + +# import essentials: +import sys, os +from math import log10 +from shutil import rmtree +from getopt import gnu_getopt as getopt +import numpy + +def printHelp(): + print Info + print "Usage: python lmp2radii.pyx test.lammpstrj\n" + return + +def makeradii(infile): + + print "Reading %s ... [WAIT]"%infile, + fin = open(infile,'r') + lines = fin.xreadlines() + print 7*"\b"+"[DONE]" + frame=0 + radii=[] + # grep the number of frames and atoms/frame + os.system("grep TIMESTEP %s | wc -l > frames; grep -m 1 -A 1 ATOMS %s > atoms"%(infile,infile)) + tmp=open("frames",'r') + frames=int(tmp.readline().split()[0]) + tmp.close() + tmp=open("atoms",'r') + atoms=int(tmp.readlines()[1].split()[0]) + tmp.close() + os.system("rm -rf frames atoms") + arry=numpy.zeros((atoms,frames),dtype=float) + framecnt=0 + header=9 + ecount=0 + print "Extracting electron radii per frame from %s ... "%(infile), + for i,line in enumerate(lines): + lo=(atoms+header)*framecnt+header + hi=lo+atoms + if (i= lo) and (i < hi): + lparse=line.split() + id=int(lparse[0]) + r=float(lparse[6]) + if (r!=0): + arry[id-1][framecnt]=r + if (framecnt==0): ecount+=1 + if (i==lo+1): + sys.stdout.write("%d/%d%s"%(framecnt+1,frames,(int(log10(framecnt+1))+3+int(log10(frames)))*"\b")) + sys.stdout.flush() + if (i == hi+1): + framecnt+=1 + print + print "Writing radii/frame table to %s ... "%(infile+'.out'), + sys.stdout.flush() + fout=open(infile+'.out','w') + for i in range(frames): + fout.writelines('\tF'+str(i)) + fout.writelines("\n") + e=1 + for a in range(atoms): + if arry[a][0] == 0.0: continue + else: + sys.stdout.write("%d/%d%s"%(e,ecount,(int(log10(e))+int(log10(ecount))+3)*"\b")) + sys.stdout.flush() + e+=1 + fout.writelines("%d\t"%(a+1)) + for f in range(frames): + fout.writelines("%f\t"%(arry[a][f])) + fout.writelines("\n") + print + print "DONE .... GOODBYE !!" + fout.close() + fin.close() + +if __name__ == '__main__': + + # set defaults + + # check for input: + opts, argv = getopt(sys.argv[1:], 'h') + + # if no input, print help and exit + if len(argv) != 1: + printHelp() + sys.exit(1) + else: + infile=argv[0] + + # read options + for opt, arg in opts: + if opt == '-h': # -h: print help + printHelp() + + makeradii(infile) diff --git a/tools/eff/lmp2radii_col.py b/tools/eff/lmp2radii_col.py new file mode 100644 index 0000000000..d5505116e9 --- /dev/null +++ b/tools/eff/lmp2radii_col.py @@ -0,0 +1,123 @@ +#!/usr/local/bin/python-2.5/bin/python + +Info=""" +Module name: lmp2radii-column.py + +Author: (c) Andres Jaramillo-Botero +California Institute of Technology +ajaramil@wag.caltech.edu +Project: pEFF +Version: August 2009 + +Extracts the electron radii from a lammps trajectory dump of style custom: + +dump 1 all custom period dump_file id type x y z spin radius ... + +NOTE: The radius must be the "column" per trajectory entry in the dump file + +""" + +# import essentials: +import sys, os +from math import log10 +from shutil import rmtree +from getopt import gnu_getopt as getopt +import numpy + +def printHelp(): + print Info + print "Usage: python lmp2radii.pyx test.lammpstrj\n" + return + +def makeradii(infile,outfile,column,True): + + print "Reading %s ... [WAIT]"%infile, + fin = open(infile,'r') + lines = fin.xreadlines() + print 7*"\b"+"[DONE]" + frame=0 + radii=[] + # grep the number of frames and atoms/frame + os.system("grep TIMESTEP %s | wc -l > frames; grep -m 1 -A 1 ATOMS %s > atoms"%(infile,infile)) + tmp=open("frames",'r') + frames=int(tmp.readline().split()[0]) + tmp.close() + tmp=open("atoms",'r') + atoms=int(tmp.readlines()[1].split()[0]) + tmp.close() + os.system("rm -rf frames atoms") + arry=numpy.zeros((atoms,frames),dtype=float) + framecnt=0 + header=9 + ecount=0 + print "Extracting electron radii per frame from %s ... "%(infile), + for i,line in enumerate(lines): + lo=(atoms+header)*framecnt+header + hi=lo+atoms + if (i= lo) and (i < hi): + lparse=line.split() + id=int(lparse[0]) + r=float(lparse[column]) + if (r!=0): + arry[id-1][framecnt]=r + if (framecnt==0): ecount+=1 + if (i==lo+1): + sys.stdout.write("%d/%d%s"%(framecnt+1,frames,(int(log10(framecnt+1))+3+int(log10(frames)))*"\b")) + sys.stdout.flush() + if (i == hi+1): + framecnt+=1 + print + print "Writing radii/frame table to %s ... "%(infile+'.out'), + sys.stdout.flush() + fout=open(outfile,'w') + for i in range(frames): + fout.writelines('\tF'+str(i)) + fout.writelines("\n") + e=1 + for a in range(atoms): + if arry[a][0] == 0.0: continue + else: + sys.stdout.write("%d/%d%s"%(e,ecount,(int(log10(e))+int(log10(ecount))+3)*"\b")) + sys.stdout.flush() + e+=1 + fout.writelines("%d\t"%(a+1)) + for f in range(frames): + fout.writelines("%f\t"%(arry[a][f])) + fout.writelines("\n") + print + print "Done !! (generated radii/frame table) \n" + fout.close() + fin.close() + +if __name__ == '__main__': + + # set defaults + outfile = "" + flag_all = False + column=6 # default = radius + + # check for input: + opts, argv = getopt(sys.argv[1:], 'c:o:ha') + + # if no input, print help and exit + if len(argv) != 1: + printHelp() + sys.exit(1) + else: + infile=argv[0] + + # read options + for opt, arg in opts: + if opt == '-h': # -h: print help + printHelp() + if opt == '-o': # output file name + outfile=arg + if opt == '-a': # all nuclii+electrons + flag_all=True + if opt == '-c': # select column from lammpstrj file to tabulate + column=int(arg) + + makeradii(infile,outfile,column,flag_all) + diff --git a/tools/eff/lmp2xyz.py b/tools/eff/lmp2xyz.py new file mode 100644 index 0000000000..704188118c --- /dev/null +++ b/tools/eff/lmp2xyz.py @@ -0,0 +1,81 @@ +Info=""" +Module name: lmp2xyz.py + +Author: (c) Andres Jaramillo-Botero +California Institute of Technology +ajaramil@caltech.edu +Project: pEFF +Version: August 2009 + +Extracts the xyz from a lammps trajectory dump of style custom: +dump 1 all custom period dump_file id type x y z spin radius ... + +Usage: python lmp2xyz.py lammps_dump_filename xyz_filename + +""" + +import os, sys +from math import log10 +from numpy import zeros + +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"} + +def lmp2xyz(lammps,xyz): + print "\nGenerating %s file"%(xyz) + fin=open(lammps,'r') + fout=open(xyz,'w') + header=9 + lines=fin.readlines() + numatoms=lines[3].split()[0] + fsize=os.system("wc -l %s> lines"%(lammps)) + tmp=open('lines','r') + tlines=tmp.readline() + tmp.close() + flines=int(tlines.split()[0]) + snaps=flines/(int(numatoms)+header) + countsnap=1 + coords=zeros((int(numatoms),4),dtype=float) + sys.stdout.write("Writing [%d]: "%(snaps)) + sys.stdout.flush() + read_atoms=1 + for line in lines: + if line.find('ITEM: TIMESTEP')==0: + read_atom_flag=False + sys.stdout.write("%d "%(countsnap)) + sys.stdout.flush() + fout.writelines("%s\nAtoms\n"%(numatoms)) + countsnap+=1 + continue + if line.find('ITEM: ATOMS')==0: + read_atom_flag=True + continue + if read_atom_flag==True: + read_atoms+=1 + parse=line.split() + if parse[0]!="": + coords[int(parse[0])-1][0]=int(parse[1]) + coords[int(parse[0])-1][1]=float(parse[2]) + coords[int(parse[0])-1][2]=float(parse[3]) + coords[int(parse[0])-1][3]=float(parse[4]) + if read_atoms==int(numatoms): + read_atoms=0 + for i in range(int(numatoms)): + 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() + fout.close() + return + +if __name__ == '__main__': + + # if no input, print help and exit + if len(sys.argv) < 2: + print Info() + sys.exit(1) + + inputfile=sys.argv[1] + outfile=sys.argv[2] + + lmp2xyz(inputfile,outfile.split()[0]) + diff --git a/tools/eff/radii.vmd b/tools/eff/radii.vmd new file mode 100644 index 0000000000..d6d211233b --- /dev/null +++ b/tools/eff/radii.vmd @@ -0,0 +1,215 @@ +# module radii.vmd +# December, 2009 -(c)- Andres Jaramillo-Botero +# Script to load variable changing radii onto a pEFF lammpstrj file + +# radii.vmd -- +# Script to read and change electron radii in vmd dynamics traj +# + +# openFile -- +# Open the file and start looking for data +# +# Arguments: +# filename Name of the file to read +# +# Result: +# infile Handle to the opened file +# +# Side effects: +# A file in question is opened. Lines containing a * or# as +# the first non-blank character are considered comments. The +# first line without this is considered to be a line with the +# names of the columns. +# +proc openFile {filename} { + set infile [open $filename "r"] + return $infile +} + +# readNames -- +# Read the names of the columns +# +# Arguments: +# infile Handle to the file +# +# Result: +# names List of names, the number indicates the number of +# the snapshot frame +# +proc readNames {infile} { + # + # Skip the header - if any + # + set pos 0 + while { [gets $infile line] >= 0 } { + if { [regexp {[ \t]*[*#]} $line] } { + incr pos + } else { + break + } + } + seek $infile 0 start + while { $pos > 0 } { + gets $infile line + incr pos -1 + } + + # + # Read the line with the column names + # + gets $infile line + + # Force the line to be interpreted as a list + set nocols [llength $line] + + return $line +} + +# readData -- +# Read the data per line +# +# Arguments: +# infile Handle to the file +# +# Result: +# values List of values, representing each column. +# A list of length zero indicates the end of file +# +proc readData {infile} { + while { [gets $infile values] == 0 } { ;# Just go on - skip empty lines } + + set nocols [llength $values] + + return $values +} + +# readFile -- +# Read the file and store the data in a (global) array +# +# Arguments: +# filename Name of the file +# +# Result: +# None +# +# Side effects: +# Filled array, ready for display +# +proc readFile {filename} { + global data_array + + set infile [openFile $filename] + + set data_array(names) [readNames $infile] + set i 0 + foreach name $data_array(names) { + set data_array($i) {} + incr i + } + + while 1 { + set values [readData $infile] + if { [llength $values] > 0 } { + set i 0 + foreach value $values { + lappend data_array($i) $value + incr i + } + } else { + break + } + } +} + +# makeXYData -- +# Make a list useable by frame-electron +# +# Arguments: +# xindex Index of frame data +# yindex Index of electron data +# +# Result: +# None +# +# Side effects: +# A dataset for changing the electron radii, per trajectory frame +# +proc makeXYData {xindex yindex} { + global data_array + + set xydata {} + foreach x $data_array($xindex) y $data_array($yindex) { + lappend xydata $x $y + } + return $xydata +} + +proc returnXYPair {x y} { + global data_array + + return [list $data_array($x) $data_array($y)] +} + +# do_radii -- +# Changes the radii of electrons per trajectory frame +# +# Arguments: +# xindex Index of frame data +# yindex Index of electron data +# +# Result: +# prints the frame:atomID:radius +# +proc do_radii {args} { + global molid data_array + + #set n [molinfo $molid get numatoms] + set f [molinfo $molid get frame] + + set fr [expr {$f+1}] + + 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 + $s set radius $nr + $s delete + #puts stderr "$fr $elec $nr" + } +} + +# main -- +# Main control flow +# + +# Check input arguments +#for {set i 0} {$i<[llength $argv]} {incr i} +# puts " - $i: [lindex $argv $i]" + +global data_array molid + +# Set input files manually +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] + +# load electron radii information for trajectory +#set datafile [lindex $::argv 1] + +set molid [mol new $xyz waitfor all] +mol modstyle 0 [molinfo top] VDW 1.0 32.0 + +puts "Starting ..." +readFile $data +puts "Read datafile and created array of radii ..." + +puts "Visualize trajectory" +trace variable vmd_frame($molid) w do_radii +animate goto start +do_radii + diff --git a/tools/eff/setup.py b/tools/eff/setup.py new file mode 100644 index 0000000000..8c6b24ade8 --- /dev/null +++ b/tools/eff/setup.py @@ -0,0 +1,12 @@ +from distutils.core import setup +from distutils.extension import Extension +from Cython.Distutils import build_ext + +# To build do: python setup.py build_ext --inplace + +ext_modules = [Extension("lmp2radii",["lmp2radii.pyx"])] +setup( + name = 'lmp2radii', + cmdclass = {'build_ext': build_ext}, + ext_modules = ext_modules +) diff --git a/tools/eff/structure_generators/Be-solid.pl b/tools/eff/structure_generators/Be-solid.pl new file mode 100755 index 0000000000..73701382b7 --- /dev/null +++ b/tools/eff/structure_generators/Be-solid.pl @@ -0,0 +1,131 @@ +#!/usr/bin/perl + +# Usage: Be-solid.pl > data.Be +# +# Generates a beryllium solid LAMMPS data file. + +$nx = shift(@ARGV); +$ny = shift(@ARGV); +$nz = shift(@ARGV); + +$La = 4.592; # eFF optimized (4.33 expt) +$Lc = 7.025; # eFF optimized (6.78 expt) + +# This part changes for different lattices +@xunit = (0, 0.5, 0, 0.5); +@yunit = (0, 0.5, 0.5 * (4/3), (1/3) * 0.5); +@zunit = (0, 0, 0.5, 0.5); + +$Lx = $La; +$Ly = $La * sqrt(3); +$Lz = $Lc; + +$idx = 0; +for ($x = 0; $x < $nx; $x++) +{ + for ($y = 0; $y < $ny; $y++) + { + for ($z = 0; $z < $nz; $z++) + { + for ($i = 0; $i <= $#xunit; $i++) + { + $xnuc[$idx] = ($x + .25) * $Lx + $xunit[$i] * $Lx; + $ynuc[$idx] = ($y + .25) * $Ly + $yunit[$i] * $Ly; + $znuc[$idx] = ($z + .25) * $Lz + $zunit[$i] * $Lz; + $idx++; + } + } + } +} + +$numnuc = $idx; + +# Print length of supercell + +printf("Created by Be-solid.pl\n\n"); +printf("%d atoms\n",$numnuc+$numnuc*2+$numnuc*2); +printf("2 atom types\n\n"); +printf("%f %f xlo xhi\n", 0, $Lx * $nx); +printf("%f %f ylo yhi\n", 0, $Ly * $ny); +printf("%f %f zlo zhi\n\n", 0, $Lz * $nz); +printf("Masses\n\n"); +printf("1 9.012182\n"); +printf("2 1.000000\n\n"); +printf("Atoms\n\n"); + +$j=0; +# Print out the nuclei +for ($i = 0; $i < $numnuc; $i++) +{ + printf("%i %i %f %f %f %f %i %f\n", $j+=1, 1, $xnuc[$i], $ynuc[$i], $znuc[$i], 4.0, 0, 0.0); +} + +# Print out the core electrons +$r_core = 0.5; +for ($i = 0; $i < $numnuc; $i++) +{ + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $xnuc[$i], $ynuc[$i], $znuc[$i], 0.0, 1, $r_core); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $xnuc[$i], $ynuc[$i], $znuc[$i], 0.0, -1, $r_core); +} + +# Print out the valence electrons +$r_valence = 2.5; +for ($i = 0; $i < $numnuc; $i += 4) +{ + $x = &BoundX($xnuc[$i] + $Lx / 2.0); + $y = &BoundY($ynuc[$i] + $Lx / (2.0 * sqrt(3))); + $z = $znuc[$i]; + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $x, $y, $z, 0.0, 1, $r_valence); + $x = &BoundX($xnuc[$i] + $Lx / 2.0); + $y = &BoundY($ynuc[$i] + $Lx / (2.0 * sqrt(3))); + $z = $znuc[$i]; + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $x, $y, $z, 0.0, -1, $r_valence); + + $x = &BoundX($xnuc[$i+1] + $Lx / 2.0); + $y = &BoundY($ynuc[$i+1] + $Lx / (2.0 * sqrt(3))); + $z = $znuc[$i+1]; + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $x, $y, $z, 0.0, 1, $r_valence); + $x = &BoundX($xnuc[$i+1] + $Lx / 2.0); + $y = &BoundY($ynuc[$i+1] + $Lx / (2.0 * sqrt(3))); + $z = $znuc[$i+1]; + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $x, $y, $z, 0.0, -1, $r_valence); + + $x = &BoundX($xnuc[$i+2] - $Lx / 2.0); + $y = &BoundY($ynuc[$i+2] - $Lx / (2.0 * sqrt(3))); + $z = $znuc[$i+2]; + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $x, $y, $z, 0.0, 1, $r_valence); + $x = &BoundX($xnuc[$i+2] - $Lx / 2.0); + $y = &BoundY($ynuc[$i+2] - $Lx / (2.0 * sqrt(3))); + $z = $znuc[$i+2]; + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $x, $y, $z, 0.0, -1, $r_valence); + + $x = &BoundX($xnuc[$i+3] - $Lx / 2.0); + $y = &BoundY($ynuc[$i+3] - $Lx / (2.0 * sqrt(3))); + $z = $znuc[$i+3]; + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $x, $y, $z, 0.0, 1, $r_valence); + $x = &BoundX($xnuc[$i+3] - $Lx / 2.0); + $y = &BoundY($ynuc[$i+3] - $Lx / (2.0 * sqrt(3))); + $z = $znuc[$i+3]; + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $x, $y, $z, 0.0, -1, $r_valence); +} + +sub BoundX { + $x = $_[0]; + if ($x > $Lx * $nx) {$x -= $Lx * $nx;} + if ($x < 0) {$x += $Lx * $nx;} + return $x; +} + +sub BoundY { + $y = $_[0]; + if ($y > $Ly * $ny) {$y -= $Ly * $ny;} + if ($y < 0) {$y += $Ly * $ny;} + return $y; +} + +sub BoundZ { + $z = $_[0]; + if ($z > $Lz * $nz) {$z -= $Lz * $nz;} + if ($z < 0) {$z += $Lz * $nz;} + return $z; +} diff --git a/tools/eff/structure_generators/Diamond.pl b/tools/eff/structure_generators/Diamond.pl new file mode 100755 index 0000000000..065e73f6d6 --- /dev/null +++ b/tools/eff/structure_generators/Diamond.pl @@ -0,0 +1,119 @@ +#!/usr/bin/perl + +# Usage: diamond > data.diamond +# +# Generates diamond A4 structure. + +$nx = shift(@ARGV); +$ny = shift(@ARGV); +$nz = shift(@ARGV); +#$scale = shift(@ARGV); + +$scale = 1.045; +$L = 7.33461; # eFF optimized (6.740 expt) +$re_core = 0.328; # core electron +$re_sigma = 1.559; # sigma electrons + +#$r_threshold = $scale * 1.6 / 0.529; # threshold for sigma bond length +$r_threshold = $scale * 1.6 / 0.5 ; # threshold for sigma bond length + +@xunit = (0, 0, 0.5, 0.5, 0.25, 0.75, 0.25, 0.75); +@yunit = (0, 0.5, 0, 0.5, 0.25, 0.75, 0.75, 0.25); +@zunit = (0, 0.5, 0.5, 0, 0.25, 0.25, 0.75, 0.75); + +$idx = 0; +for ($x = 0; $x < $nx; $x++) +{ + for ($y = 0; $y < $ny; $y++) + { + for ($z = 0; $z < $nz; $z++) + { + for ($i = 0; $i <= $#xunit; $i++) + { + $xnuc[$idx] = $x * $L + $xunit[$i] * $L; + $ynuc[$idx] = $y * $L + $yunit[$i] * $L; + $znuc[$idx] = $z * $L + $zunit[$i] * $L; + $idx++; + } + } + } +} + +$numnuc = $idx; +$xx = $L * $nx; +$yy = $L * $ny; +$zz = $L * $nz; + +# Print length of supercell + +printf("Created with Diamond.pl\n\n"); +printf("%d atoms\n",$numnuc*7); +printf("2 atom types\n\n"); +printf("%f %f xlo xhi\n", 0, $L * $nx); +printf("%f %f ylo yhi\n", 0, $L * $ny); +printf("%f %f zlo zhi\n\n", 0, $L * $nz); +printf("Masses\n\n"); +printf("1 12.01070\n"); +printf("2 1.000000\n\n"); +printf("Atoms\n\n"); + +# Print out the nuclei and the core electrons +for ($i = 0; $i < $numnuc; $i++) +{ + printf("%i %i %f %f %f %f 0 0.0\n", $j+=1, 1, $xnuc[$i], $ynuc[$i], $znuc[$i], 6.0); +} + +for ($i = 0; $i < $numnuc; $i++) +{ + printf("%i %i %f %f %f 0.0 %i %.10f\n", $j+=1, 2, $xnuc[$i], $ynuc[$i], $znuc[$i], 1, $re_core); + printf("%i %i %f %f %f 0.0 %i %.10f\n", $j+=1, 2, $xnuc[$i], $ynuc[$i], $znuc[$i], -1, $re_core); +} + +# Print out sigma electrons + +$LLx = $L * $nx; +$LLy = $L * $ny; +$LLz = $L * $nz; + +$k=$j; +for ($i = 0; $i < $numnuc; $i++) +{ + for ($j = 0; $j < $i; $j++) + { + $x = $xnuc[$j] - $xnuc[$i]; + $y = $ynuc[$j] - $ynuc[$i]; + $z = $znuc[$j] - $znuc[$i]; + + # Minimum image convention + + if ($x > $LLx/2) {$x -= $LLx;} + if ($y > $LLy/2) {$y -= $LLy;} + if ($z > $LLz/2) {$z -= $LLz;} + + if ($x < -$LLx/2) {$x += $LLx;} + if ($y < -$LLy/2) {$y += $LLy;} + if ($z < -$LLz/2) {$z += $LLz;} + + $r = sqrt($x * $x + $y * $y + $z * $z); + if ($r < $r_threshold) + { + $bond_x = $xnuc[$i] + $x / 2; + $bond_y = $ynuc[$i] + $y / 2; + $bond_z = $znuc[$i] + $z / 2; + + # Minimum image convention + + if ($bond_x > $LLx) {$bond_x -= $LLx}; + if ($bond_y > $LLy) {$bond_y -= $LLy}; + if ($bond_z > $LLz) {$bond_z -= $LLz}; + + if ($bond_x < 0) {$bond_x += $LLx}; + if ($bond_y < 0) {$bond_y += $LLy}; + if ($bond_z < 0) {$bond_z += $LLz}; + + printf("%i %i %f %f %f 0.0 %i %.10f\n", $k+=1, 2, $bond_x, $bond_y, $bond_z, 1, $re_sigma); + printf("%i %i %f %f %f 0.0 %i %.10f\n", $k+=1, 2, $bond_x, $bond_y, $bond_z, -1, $re_sigma); + } + } +} + diff --git a/tools/eff/structure_generators/Li-hydride.pl b/tools/eff/structure_generators/Li-hydride.pl new file mode 100755 index 0000000000..c18eafe105 --- /dev/null +++ b/tools/eff/structure_generators/Li-hydride.pl @@ -0,0 +1,93 @@ +#!/usr/bin/perl + +# Usage: ./Li-hydride.pl > data.Li-hydride +# +# Generates a lithium hydride solid. + +$nx = shift(@ARGV); +$ny = shift(@ARGV); +$nz = shift(@ARGV); + +$L = 6.785; # eFF optimized (7.72 expt) + +# This part changes for different lattices +@xunit = (0, 0.5, 0, 0.5, 0.5, 0, 0, 0.5); +@yunit = (0, 0.5, 0.5, 0, 0, 0.5, 0, 0.5); +@zunit = (0, 0, 0.5, 0.5, 0, 0, 0.5, 0.5); + +$r_elec = 0.7; +$r2_elec = 2.2; + +$Lx = $L; +$Ly = $L; +$Lz = $L; + +$idx = 0; +for ($x = 0; $x < $nx; $x++) +{ + for ($y = 0; $y < $ny; $y++) + { + for ($z = 0; $z < $nz; $z++) + { + for ($i = 0; $i <= $#xunit; $i++) + { + $xnuc[$idx] = $x * $Lx + $xunit[$i] * $L + 0.5 * $L; + $ynuc[$idx] = $y * $Ly + $yunit[$i] * $L + 0.5 * $L; + $znuc[$idx] = $z * $Lz + $zunit[$i] * $L + 0.5 * $L; + $idx++; + } + } + } +} + +$numnuc = $idx; + +# Print length of supercell + +printf("Created with Li-hydride.pl\n\n"); +printf("%d atoms\n",$numnuc+$numnuc+$numnuc); +printf("3 atom types\n\n"); +printf("%f %f xlo xhi\n", 0, $Lx * $nx); +printf("%f %f ylo yhi\n", 0, $Ly * $ny); +printf("%f %f zlo zhi\n\n", 0, $Lz * $nz); +printf("Masses\n\n"); +printf("1 6.941000\n"); +printf("2 1.007940\n"); +printf("3 1.000000\n\n"); +printf("Atoms\n\n"); + +$j = 0; +# Print out the nuclei +for ($i = 0; $i < $numnuc; $i += 8) +{ + printf("%i %i %f %f %f %f %i %f\n", $j+=1, 1, $xnuc[$i], $ynuc[$i], $znuc[$i], 3.0, 0, 0.0); + printf("%i %i %f %f %f %f %i %f\n", $j+=1, 1, $xnuc[$i+1], $ynuc[$i+1], $znuc[$i+1], 3.0, 0, 0.0); + printf("%i %i %f %f %f %f %i %f\n", $j+=1, 1, $xnuc[$i+2], $ynuc[$i+2], $znuc[$i+2], 3.0, 0, 0.0); + printf("%i %i %f %f %f %f %i %f\n", $j+=1, 1, $xnuc[$i+3], $ynuc[$i+3], $znuc[$i+3], 3.0, 0, 0.0); + printf("%i %i %f %f %f %f %i %f\n", $j+=1, 2, $xnuc[$i+4], $ynuc[$i+4], $znuc[$i+4], 1.0, 0, 0.0); + printf("%i %i %f %f %f %f %i %f\n", $j+=1, 2, $xnuc[$i+5], $ynuc[$i+5], $znuc[$i+5], 1.0, 0, 0.0); + printf("%i %i %f %f %f %f %i %f\n", $j+=1, 2, $xnuc[$i+6], $ynuc[$i+6], $znuc[$i+6], 1.0, 0, 0.0); + printf("%i %i %f %f %f %f %i %f\n", $j+=1, 2, $xnuc[$i+7], $ynuc[$i+7], $znuc[$i+7], 1.0, 0, 0.0); +} + +# Print out the electrons +for ($i = 0; $i < $numnuc; $i += 8) +{ + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i ], $ynuc[$i ], $znuc[$i ], 0.0, 1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i ], $ynuc[$i ], $znuc[$i ], 0.0, -1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i+1], $ynuc[$i+1], $znuc[$i+1], 0.0, 1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i+1], $ynuc[$i+1], $znuc[$i+1], 0.0, -1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i+2], $ynuc[$i+2], $znuc[$i+2], 0.0, 1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i+2], $ynuc[$i+2], $znuc[$i+2], 0.0, -1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i+3], $ynuc[$i+3], $znuc[$i+3], 0.0, 1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i+3], $ynuc[$i+3], $znuc[$i+3], 0.0, -1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i+4], $ynuc[$i+4], $znuc[$i+4], 0.0, 1, $r2_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i+4], $ynuc[$i+4], $znuc[$i+4], 0.0, -1, $r2_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i+5], $ynuc[$i+5], $znuc[$i+5], 0.0, 1, $r2_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i+5], $ynuc[$i+5], $znuc[$i+5], 0.0, -1, $r2_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i+6], $ynuc[$i+6], $znuc[$i+6], 0.0, 1, $r2_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i+6], $ynuc[$i+6], $znuc[$i+6], 0.0, -1, $r2_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i+7], $ynuc[$i+7], $znuc[$i+7], 0.0, 1, $r2_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 3, $xnuc[$i+7], $ynuc[$i+7], $znuc[$i+7], 0.0, -1, $r2_elec); +} + diff --git a/tools/eff/structure_generators/Li-solid.pl b/tools/eff/structure_generators/Li-solid.pl new file mode 100755 index 0000000000..a3efb8133e --- /dev/null +++ b/tools/eff/structure_generators/Li-solid.pl @@ -0,0 +1,92 @@ +#!/usr/bin/perl + +# Usage: Li-solid.pl > data.Li +# +# Generates a lithium solid LAMMPS data input file +# with FCC nuclear positions and interstitial electron positions. + +$nx = shift(@ARGV); +$ny = shift(@ARGV); +$nz = shift(@ARGV); + +$L = 8.352; # eFF optimized (8.32 expt) + +# This part changes for different lattices +@xunit = (0, 0.5, 0, 0.5, 0.5, 0, 0, 0.5); +@yunit = (0, 0.5, 0.5, 0, 0, 0.5, 0, 0.5); +@zunit = (0, 0, 0.5, 0.5, 0, 0, 0.5, 0.5); + +$r_elec = 0.7; +$r_elec2 = 3.0; + +$Lx = $L; +$Ly = $L; +$Lz = $L; + +$idx = 0; +for ($x = 0; $x < $nx; $x++) +{ + for ($y = 0; $y < $ny; $y++) + { + for ($z = 0; $z < $nz; $z++) + { + for ($i = 0; $i <= $#xunit; $i++) + { + $xnuc[$idx] = $x * $Lx + $xunit[$i] * $L + 0.5 * $L; + $ynuc[$idx] = $y * $Ly + $yunit[$i] * $L + 0.5 * $L; + $znuc[$idx] = $z * $Lz + $zunit[$i] * $L + 0.5 * $L; + $idx++; + } + } + } +} + +$numnuc = $idx; + +# Print length of supercell + +printf("Created by AJB\n\n"); +printf("%d atoms\n",2*$numnuc); +printf("2 atom types\n\n"); +printf("%f %f xlo xhi\n", 0, $Lx * $nx); +printf("%f %f ylo yhi\n", 0, $Ly * $ny); +printf("%f %f zlo zhi\n\n", 0, $Lz * $nz); +printf("Masses\n\n"); +printf("1 6.941000\n"); +printf("2 1.000000\n\n"); +printf("Atoms\n\n"); + +$j = 0; +# Print out the nuclei +for ($i = 0; $i < $numnuc; $i += 8) +{ + printf("%i %i %f %f %f %f %i %f\n", $j+=1,1,$xnuc[$i], $ynuc[$i], $znuc[$i], 3.0, 0, 0.0); + printf("%i %i %f %f %f %f %i %f\n", $j+=1,1,$xnuc[$i+1], $ynuc[$i+1], $znuc[$i+1], 3.0, 0, 0.0); + printf("%i %i %f %f %f %f %i %f\n", $j+=1,1,$xnuc[$i+2], $ynuc[$i+2], $znuc[$i+2], 3.0,0,0.0); + printf("%i %i %f %f %f %f %i %f\n", $j+=1,1,$xnuc[$i+3], $ynuc[$i+3], $znuc[$i+3], 3.0,0,0.0); +} + +# Print out the core electrons +for ($i = 0; $i < $numnuc; $i += 8) +{ + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $xnuc[$i ], $ynuc[$i ], $znuc[$i ], 0.0, 1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $xnuc[$i ], $ynuc[$i ], $znuc[$i ], 0.0, -1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $xnuc[$i+1], $ynuc[$i+1], $znuc[$i+1], 0.0, 1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $xnuc[$i+1], $ynuc[$i+1], $znuc[$i+1], 0.0, -1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $xnuc[$i+2], $ynuc[$i+2], $znuc[$i+2], 0.0, 1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $xnuc[$i+2], $ynuc[$i+2], $znuc[$i+2], 0.0, -1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $xnuc[$i+3], $ynuc[$i+3], $znuc[$i+3], 0.0, 1, $r_elec); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $xnuc[$i+3], $ynuc[$i+3], $znuc[$i+3], 0.0, -1, $r_elec); +} + +# Print out the valence electrons +for ($i = 0; $i < $numnuc; $i += 8) +{ + if (rand() < .5) {$spin = 1;} else {$spin = -1;} + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $xnuc[$i+4], $ynuc[$i+4], $znuc[$i+4], 0.0, $spin, $r_elec2); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $xnuc[$i+5], $ynuc[$i+5], $znuc[$i+5], 0.0, -$spin, $r_elec2); + if (rand() < .5) {$spin = 1;} else {$spin = -1;} + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $xnuc[$i+6], $ynuc[$i+6], $znuc[$i+6], 0.0, $spin, $r_elec2); + printf("%i %i %f %f %f %f %i %.10f\n", $j+=1, 2, $xnuc[$i+7], $ynuc[$i+7], $znuc[$i+7], 0.0, -$spin, $r_elec2); +} + diff --git a/tools/eff/structure_generators/Uniform-electron-gas.pl b/tools/eff/structure_generators/Uniform-electron-gas.pl new file mode 100755 index 0000000000..91186fbdab --- /dev/null +++ b/tools/eff/structure_generators/Uniform-electron-gas.pl @@ -0,0 +1,67 @@ +#!/usr/bin/perl + +# Usage: ./Uniform-electron-gas.pl > data.uniform-e-gas +# +# Generates a uniform electron gas using electrons on an NaCl lattice. + +$nx = shift(@ARGV); +$ny = shift(@ARGV); +$nz = shift(@ARGV); +$rs = shift(@ARGV); + +# This part changes for different lattices +@xunit = (0, 0.5, 0.5, 0, 0, 0.5, 0.5, 0); +@yunit = (0, 0, 0.5, 0.5, 0.5, 0.5, 0, 0); +@zunit = (0, 0, 0, 0, 0.5, 0.5, 0.5, 0.5); +$volume = 1; +$elecs_per_cell = 8; + +$L = $rs * ((4/3) * 3.14159265 * $elecs_per_cell / $volume) ** (1/3); # length of unit cell +$r_elec = $rs * sqrt(1.5 / 1.1050); + +$Lx = $L; +$Ly = $L; +$Lz = $L; + +$idx = 0; +for ($x = 0; $x < $nx; $x++) +{ + for ($y = 0; $y < $ny; $y++) + { + for ($z = 0; $z < $nz; $z++) + { + for ($i = 0; $i <= $#xunit; $i++) + { + $xnuc[$idx] = $x * $Lx + $xunit[$i] * $L; + $ynuc[$idx] = $y * $Ly + $yunit[$i] * $L; + $znuc[$idx] = $z * $Lz + $zunit[$i] * $L; + $idx++; + } + } + } +} + +$numnuc = $idx; + +# Print length of supercell + +printf("Created with Uniform-electron-gas.pl\n\n"); +printf("%d atoms\n",$numnuc); +printf("1 atom types\n\n"); +printf("%f %f xlo xhi\n", 0, $Lx * $nx); +printf("%f %f ylo yhi\n", 0, $Ly * $ny); +printf("%f %f zlo zhi\n\n", 0, $Lz * $nz); +printf("Masses\n\n"); +printf("1 1.000000\n\n"); +printf("Atoms\n\n"); + +$j = 0; + +# Print out the electrons +for ($i = 0; $i < $numnuc; $i += 2) +{ + printf("%i %i %i %f %f %f %.10f\n", $j+=1, 1, 1, $r_elec, $xnuc[$i], $ynuc[$i], $znuc[$i]); + printf("%i %i %i %f %f %f %.10f\n", $j+=1, 1, -1, $r_elec, $xnuc[$i+1], $ynuc[$i+1], $znuc[$i+1]); +} + +printf("\n"); diff --git a/tools/eff/structure_generators/h2.pl b/tools/eff/structure_generators/h2.pl new file mode 100755 index 0000000000..99645e0cd7 --- /dev/null +++ b/tools/eff/structure_generators/h2.pl @@ -0,0 +1,67 @@ +#!/usr/bin/perl + +# Usage: h2.pl > data.h2 +# +# Generates rectangular lattice of hydrogen atoms, # in each direction = nx, +# with Wigner radius rs. +# ... +# Shifts H atoms in alternating directions so they form H2 molecule +# starting structures. + +$nx = shift(@ARGV); +$ny = shift(@ARGV); +$nz = shift(@ARGV); +$rs = shift(@ARGV); + +$L = 1.6119919540164693 * $rs; # length of unit cell ((4/3 pi)^(1/3) +$re = 1.823572; # electron radius + +$dshift = 0.5; + +$idx = 0; +for ($x = 0; $x < $nx; $x++) +{ + for ($y = 0; $y < $ny; $y++) + { + $dsign = 1; + for ($z = 0; $z < $nz; $z++) + { + $xnuc[$idx] = $x * $L + 0.5 * $L; + $ynuc[$idx] = $y * $L + 0.5 * $L; + $znuc[$idx] = $z * $L + 0.5 * $L + $dshift * $dsign; + $dsign = -$dsign; + $idx++; + } + } +} + +$numnuc = $idx; + +# Print length of supercell + +printf("Created with h2.pl\n\n"); +printf("%d atoms\n",$numnuc*2); +printf("2 atom types\n\n"); +printf("%f %f xlo xhi\n", 0, $L * $nx); +printf("%f %f ylo yhi\n", 0, $L * $ny); +printf("%f %f zlo zhi\n\n", 0, $L * $nz); +printf("Masses\n\n"); +printf("1 1.007940\n"); +printf("2 1.000000\n\n"); +printf("Atoms\n\n"); + +$j=0; + +# Print out the nuclei and the core electrons +for ($i = 0; $i < $numnuc; $i++) +{ + printf("%i %i %f %f %f %f %i %f\n", $j+=1, 1, $xnuc[$i], $ynuc[$i], $znuc[$i], 1.0, 0, 0.0); +} + +$spin = 1; +for ($i = 0; $i < $numnuc; $i++) +{ + if ($spin == 1) {$spin = -1;} else {$spin = 1;} + printf("%i %i %f %f %f %f %i %f\n", $j+=1, 2, $xnuc[$i], $ynuc[$i], $znuc[$i], 0.0, $spin, $re); +} +