mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5713 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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Info="""
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Module name: bohr2ang.py
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Author: (c) Andres Jaramillo-Botero
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California Institute of Technology
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ajaramil@caltech.edu
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Project: pEFF
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Version: August 2009
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Usage: python bohr2ang.py
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>>Name of data file (bohr): [datafile]
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Results:
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creates a datafile with extension .ang in real units
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"""
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import os
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currdir=os.getcwd()
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datafile=raw_input("Name of data file (bohr): ")
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bohr2ang=0.529177249
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bperatu2angperfs=0.512396271120794
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f=open(currdir+'/'+datafile,'r')
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w=open(currdir+'/'+datafile+'.ang','w')
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lines=f.readlines()
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atom_flag=False
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vel_flag=False
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for line in lines:
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if line.find("xlo") > 0:
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parse=line.split()
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w.write("%f %f xlo xhi\n"%(float(parse[0])*bohr2ang,float(parse[1])*bohr2ang))
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elif line.find("ylo") > 0:
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parse=line.split()
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w.write("%f %f ylo yhi\n"%(float(parse[0])*bohr2ang,float(parse[1])*bohr2ang))
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elif line.find("zlo") > 0:
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parse=line.split()
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w.write("%f %f zlo zhi\n"%(float(parse[0])*bohr2ang,float(parse[1])*bohr2ang))
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elif line.find("xy") >= 0:
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parse=line.split()
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w.write("%f %f %f xy xz yz\n"%(float(parse[0])*bohr2ang,float(parse[1])*bohr2ang,float(parse[2])*bohr2ang))
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elif atom_flag and line.strip():
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parse=line.split()
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id=parse[0]
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type=parse[1]
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q=parse[2]
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spin=parse[3]
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eradius=float(parse[4])*bohr2ang
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x=float(parse[5])*bohr2ang
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y=float(parse[6])*bohr2ang
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z=float(parse[7])*bohr2ang
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rest=" ".join(parse[8:])
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w.write("%s %s %s %s %f %f %f %f %s\n"%(id,type,q,spin,eradius,x,y,z,rest))
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elif line.find("Atoms") >= 0:
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w.write(line)
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atom_flag=True
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continue
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elif vel_flag and line != "\n":
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parse=line.split()
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id=parse[0]
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vx=float(parse[1])*bperatu2angperfs
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vy=float(parse[2])*bperatu2angperfs
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vz=float(parse[3])*bperatu2angperfs
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erv=float(parse[4])*bperatu2angperfs
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w.write("%s %f %f %f\n"%(id,vx,vy,vz,erv))
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elif line.find("Velocities") >= 0:
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w.write(line)
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atom_flag=False
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vel_flag=True
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continue
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else:
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w.write(line)
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f.close()
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w.close()
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File diff suppressed because it is too large
Load Diff
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#!/usr/bin/perl
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# Usage: Li-solid.pl <nx> <ny> <nz> > data.Li
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#
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# Generates a lithium solid LAMMPS data input file
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# with FCC nuclear positions and interstitial electron positions.
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$nx = shift(@ARGV);
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$ny = shift(@ARGV);
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$nz = shift(@ARGV);
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$L = 4.419688383648; # eFF optimized (8.32 expt)
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# This part changes for different lattices
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@xunit = (0, 0.2645886245, 0, 0.2645886245, 0.2645886245, 0, 0, 0.2645886245);
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@yunit = (0, 0.2645886245, 0.2645886245, 0, 0, 0.2645886245, 0, 0.2645886245);
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@zunit = (0, 0, 0.2645886245, 0.2645886245, 0, 0, 0.2645886245, 0.2645886245);
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$r_elec = 0.3704240743;
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$r_elec2 = 1.587531747;
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$Lx = $L;
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$Ly = $L;
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$Lz = $L;
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$idx = 0;
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for ($x = 0; $x < $nx; $x++)
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{
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for ($y = 0; $y < $ny; $y++)
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{
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for ($z = 0; $z < $nz; $z++)
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{
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for ($i = 0; $i <= $#xunit; $i++)
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{
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$xnuc[$idx] = $x * $Lx + $xunit[$i] * $L + 0.2645886245 * $L;
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$ynuc[$idx] = $y * $Ly + $yunit[$i] * $L + 0.2645886245 * $L;
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$znuc[$idx] = $z * $Lz + $zunit[$i] * $L + 0.2645886245 * $L;
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$idx++;
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}
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}
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}
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}
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$numnuc = $idx;
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# Print length of supercell
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printf("Created by AJB\n\n");
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printf("%d atoms\n",2*$numnuc);
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printf("2 atom types\n\n");
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printf("%f %f xlo xhi\n", 0, $Lx * $nx);
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printf("%f %f ylo yhi\n", 0, $Ly * $ny);
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printf("%f %f zlo zhi\n\n", 0, $Lz * $nz);
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printf("Masses\n\n");
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printf("1 6.941000\n");
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printf("2 1.000000\n\n");
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printf("Atoms\n\n");
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$j = 0;
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# Print out the nuclei
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for ($i = 0; $i < $numnuc; $i += 8)
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{
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printf("%i %i %f %i %f %f %f %f\n", $j+=1,1,3.0, 0, 0.0,$xnuc[$i], $ynuc[$i], $znuc[$i]);
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printf("%i %i %f %i %f %f %f %f\n", $j+=1,1,3.0, 0, 0.0,$xnuc[$i+1], $ynuc[$i+1], $znuc[$i+1]);
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printf("%i %i %f %i %f %f %f %f\n", $j+=1,1,3.0, 0, 0.0,$xnuc[$i+2], $ynuc[$i+2], $znuc[$i+2]);
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printf("%i %i %f %i %f %f %f %f\n", $j+=1,1,3.0, 0, 0.0,$xnuc[$i+3], $ynuc[$i+3], $znuc[$i+3]);
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}
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# Print out the core electrons
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for ($i = 0; $i < $numnuc; $i += 8)
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{
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printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, 1, $r_elec,$xnuc[$i ], $ynuc[$i ], $znuc[$i ]);
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printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, -1, $r_elec,$xnuc[$i ], $ynuc[$i ], $znuc[$i ]);
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printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, 1, $r_elec,$xnuc[$i+1], $ynuc[$i+1], $znuc[$i+1]);
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printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, -1, $r_elec,$xnuc[$i+1], $ynuc[$i+1], $znuc[$i+1]);
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printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, 1, $r_elec,$xnuc[$i+2], $ynuc[$i+2], $znuc[$i+2]);
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printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, -1, $r_elec,$xnuc[$i+2], $ynuc[$i+2], $znuc[$i+2]);
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printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, 1, $r_elec,$xnuc[$i+3], $ynuc[$i+3], $znuc[$i+3]);
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printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, -1, $r_elec,$xnuc[$i+3], $ynuc[$i+3], $znuc[$i+3]);
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}
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# Print out the valence electrons
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for ($i = 0; $i < $numnuc; $i += 8)
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{
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if (rand() < .5) {$spin = 1;} else {$spin = -1;}
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printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, $spin, $r_elec2,$xnuc[$i+4], $ynuc[$i+4], $znuc[$i+4]);
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printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, -$spin, $r_elec2,$xnuc[$i+5], $ynuc[$i+5], $znuc[$i+5]);
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if (rand() < .5) {$spin = 1;} else {$spin = -1;}
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printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, $spin, $r_elec2,$xnuc[$i+6], $ynuc[$i+6], $znuc[$i+6]);
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printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, -$spin, $r_elec2,$xnuc[$i+7], $ynuc[$i+7], $znuc[$i+7]);
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}
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