Esempio n. 1
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def unFractional(posfile):
    [basis,atypes,atoms,head,poscar] = poscarIO.read(open(posfile,"r").readlines(),frac_coord=True)
    xs,ys,zs = zip(*atoms)
    if sum(xs)/len(xs)>1.0 or sum(ys)/len(ys)>1.0 or sum(zs)/len(zs)>1.0:
        print "Error: it appears these are already unfractional coordinates. %s"%posfile
        exit(0)
    [basis,atypes,atoms,head,poscar] = poscarIO.read(open(posfile,"r").readlines(),frac_coord=False)
    poscarIO.write(posfile,basis, atoms,atypes,head,frac=True,autoFrac=False)
Esempio n. 2
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def fractional(posfile):
    [basis,atypes,atoms,head,poscar] = poscarIO.read(open(posfile,"r").readlines(),frac_coord=True)
    fraced=False
    xs,ys,zs = zip(*atoms)
    if sum(xs)/len(xs)>1.0 or sum(ys)/len(ys)>1.0 or sum(zs)/len(zs)>1.0:
        fraced=True
    if not fraced:
        print "Error: it appears these are already fractional coordiantes. %s"%posfile
        exit(0)
    poscarIO.write(posfile,basis,atoms,atypes,head,frac=True)
Esempio n. 3
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def fractional(posfile):
    [basis, atypes, atoms, head, poscar] = poscarIO.read(open(posfile,
                                                              "r").readlines(),
                                                         frac_coord=True)
    fraced = False
    xs, ys, zs = zip(*atoms)
    if sum(xs) / len(xs) > 1.0 or sum(ys) / len(ys) > 1.0 or sum(zs) / len(
            zs) > 1.0:
        fraced = True
    if not fraced:
        print "Error: it appears these are already fractional coordiantes. %s" % posfile
        exit(0)
    poscarIO.write(posfile, basis, atoms, atypes, head, frac=True)
Esempio n. 4
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def unFractional(posfile):
    [basis, atypes, atoms, head, poscar] = poscarIO.read(open(posfile,
                                                              "r").readlines(),
                                                         frac_coord=True)
    xs, ys, zs = zip(*atoms)
    if sum(xs) / len(xs) > 1.0 or sum(ys) / len(ys) > 1.0 or sum(zs) / len(
            zs) > 1.0:
        print "Error: it appears these are already unfractional coordinates. %s" % posfile
        exit(0)
    [basis, atypes, atoms, head, poscar] = poscarIO.read(open(posfile,
                                                              "r").readlines(),
                                                         frac_coord=False)
    poscarIO.write(posfile,
                   basis,
                   atoms,
                   atypes,
                   head,
                   frac=True,
                   autoFrac=False)
Esempio n. 5
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def outcar2poscar(outcar,outposcar,wantconfig):
    basis,atypes,atoms,head,poscar = outcarIO.outcar2poscar(outcar,wantconfig)
    poscarIO.write(outposcar,basis,atoms,atypes,head)
Esempio n. 6
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def prompt_iface(md, count, stresskb, T, PE, KE, ax, ay, az, afx, afy, afz, v1,
                 v2, v3, types):
    print "=" * 50
    print "Step Number: %d" % (count)
    print "Stress (in kB) XX YY ZZ XY YZ XZ:"
    print stresskb
    if md == True:
        print "T=%g,   PE=%g,   TE=%g" % (T, PE, KE)
    else:
        print "PE=%g" % (PE)
    print "=" * 50
    print ""

    if not (plotdisabled):
        athread = threading.Thread(target=plot3,
                                   args=(md, ax, ay, az, afx, afy, afz, v1, v2,
                                         v3, types))
        athread.start()
        athread.join()
    while True:
        try:
            val = raw_input(
                "Input coords and radius of sphere (x y z r) or (Enter) to continue:\n"
            )
            [rx, ry, rz, rr] = [float(k) for k in val.split()]
            N = len(ax)
            atoms = [[ax[i], ay[i], az[i], types[i]] for i in range(N)
                     if sqrt((ax[i] - rx)**2 + (ay[i] - ry)**2 +
                             (az[i] - rz)**2) <= rr]
            atoms.sort(key=lambda x: x[3])
            d1, d2, d3, types = zip(*atoms)
            cs = [types.count(i) for i in range(max(types) + 1)]

            while True:
                try:
                    val = float(
                        raw_input(
                            "Scale factor (increases vacuum around cluster): \n"
                        ))
                except ValueError:
                    print "Scaling factor should be a floating point value between 1.2 and 3.0."
                else:
                    break

            for atom in atoms:
                print "% 5.5g  % 5.5g  % 5.5g" % (tuple(atom[:3]))

            poscarIO.write("POSCAR.CLUSTER%d" % len(atoms),
                           array([v1, v2, v3]) * val,
                           [atom[:3] for atom in atoms], cs,
                           "Cluster genearted by grabcluster.py")
            print "POSCAR.CLUSTER%d written to." % len(atoms)
            exit(0)

        except ValueError:
            if len(val) == 0:
                break
        else:
            if not (plotdisabled):
                bthread = threading.Thread(target=plot3sphere,
                                           args=(md, ax, ay, az, afx, afy, afz,
                                                 v1, v2, v3, rx, ry, rz, rr))
                bthread.start()
                bthread.join()
                try:
                    val = raw_input("Good? (y/n):")
                    if val == "y" or val == "Y":

                        N = len(ax)
                        atoms = [[ax[i], ay[i], az[i], types[i]]
                                 for i in range(N)
                                 if sqrt((ax[i] - rx)**2 + (ay[i] - ry)**2 +
                                         (az[i] - rz)**2) <= rr]

                        atoms.sort(key=lambda x: x[3])
                        d1, d2, d3, types = zip(*atoms)
                        cs = [types.count(i) for i in range(N)]
                        #cut off types list after last non-zero number
                        last = 0
                        for i, v in enumerate(cs):
                            if v > 0:
                                last = i
                        cs = cs[:last + 1]
                        print cs[:]
                        for atom in atoms:
                            print "% 5.5g  % 5.5g  % 5.5g" % (tuple(atom[:3]))

                        exit(0)
                except ValueError:
                    pass
Esempio n. 7
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    atype = [0] * natom
    ax = [0.0] * natom
    ay = [0.0] * natom
    az = [0.0] * natom
    afx = [0.0] * natom
    afy = [0.0] * natom
    afz = [0.0] * natom
    for i in range(natom):
        line = forcedb.readline().split()
        atype[i] = int(line[0])
        [ax[i], ay[i], az[i], afx[i], afy[i],
         afz[i]] = [float(j) for j in line[1:7]]

    if (count == confignum):
        pcar = sys.argv[3]
        poscarIO.write(pcar, array(basis), zip(ax, ay, az), atype, head)
        """
        wrt=pcar+" "+msg+"\n"
        wrt+="1.0\n"
        wrt+=boundx+"\n"
        wrt+=boundy+"\n"
        wrt+=boundz+"\n"
        
        types=[atype.count(u) for u in set(atype)]
        wrt+=" ".join(map(str,types))+"\n"#type information
        wrt+="Direct\n"

        a=array([bndx,bndy,bndz])
        for b in zip(ax,ay,az):
            x=linalg.solve(a.transpose(),b)
            wrt+="%9.9f %9.9f %9.9f\n"%(x[0],x[1],x[2])
Esempio n. 8
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def poscarGrow(poscarName,outputName,cx,cy,cz):
    poscar=open(poscarName,"r").readlines()
    nCopies=cx*cy*cz
 
    [basis,atypes,atoms,head,poscar] = poscarIO.read(poscar,frac_coord=True)
    natoms=len(atoms)
    v1,v2,v3=map(array,basis)
    ax,ay,az=map(array,zip(*atoms))

    #duplicate and tile
    ax=array(split(tile(ax,nCopies),nCopies))
    ay=array(split(tile(ay,nCopies),nCopies))
    az=array(split(tile(az,nCopies),nCopies))

    #Shift tiles in x dirn
    shift=array([1]*natoms)
    shiftfull=array([shift*j for j in range(cx)])
    for i in range(cy*cz):
        ax[i*cx+array(range(cx))]+=shiftfull

    #Shift tiles in y dirn
    shift=array([1]*natoms)
    shiftfull=array([shift*(j/cx) for j in range(cy*cx)])
    for i in range(cz):
        ay[i*cx*cy+array(range(cy*cx))]+=shiftfull

    #Shift tiles in z dirn
    shift=array([1]*natoms)
    shiftfull=array([shift*(j/cx/cy) for j in range(cy*cx*cz)])
    az+=shiftfull

    ax=ax.reshape([nCopies*natoms])
    ay=ay.reshape([nCopies*natoms])
    az=az.reshape([nCopies*natoms])
    
    #need to normalize with new positions with respect to duplicated lattice params
    v1*=cx
    v2*=cy
    v3*=cz
    basis=[v1,v2,v3]
    A=matrix([[float(cx),0.0,0.0],[0.0,float(cy),0.0],[0.0,0.0,float(cz)]])
    ax,ay,az=zip(*[linalg.solve(A,array(p).T)[:] for p in zip(ax,ay,az)])

#    if max(ax)>1.0 or max(ay)>1.0 or max(az)>1.0:
#        continue
#        exit(0)

    atoms=zip(ax,ay,az)

    #Sort atoms by type, as required by POSCAR
    types=list()
    j=0
    for i in atypes:
        types+=[j+1]*i
        j+=1
    newtypes=types*cx*cy*cz

    atoms,types=zip(*sorted(zip(atoms,newtypes),key=lambda x:x[1]))
    atypes=[i*nCopies for i in atypes]

    poscarIO.write(outputName,basis,atoms,atypes,head)
    return len(atoms),basis
Esempio n. 9
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    forcedb.readline() #The #F
    atype=[0]*natom
    ax=[0.0]*natom
    ay=[0.0]*natom
    az=[0.0]*natom
    afx=[0.0]*natom
    afy=[0.0]*natom
    afz=[0.0]*natom
    for i in range(natom):
        line=forcedb.readline().split()
        atype[i]=int(line[0])
        [ax[i],ay[i],az[i],afx[i],afy[i],afz[i]]=[float(j) for j in line[1:7]]

    if(count==confignum):
        pcar=sys.argv[3]
        poscarIO.write(pcar,array(basis),zip(ax,ay,az),atype,head)

        """
        wrt=pcar+" "+msg+"\n"
        wrt+="1.0\n"
        wrt+=boundx+"\n"
        wrt+=boundy+"\n"
        wrt+=boundz+"\n"
        
        types=[atype.count(u) for u in set(atype)]
        wrt+=" ".join(map(str,types))+"\n"#type information
        wrt+="Direct\n"

        a=array([bndx,bndy,bndz])
        for b in zip(ax,ay,az):
            x=linalg.solve(a.transpose(),b)
Esempio n. 10
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    exit(0)

#Gather poscar information for last set of atoms
basis, atypes, atoms, head, poscar = outcarIO.outcar2poscar(
    outcarFile, configRequest)


#Convert from fractional units to cartesian
def u2a(u):
    a = list()
    a.append(u[0] * basis[0][0] + u[0] * basis[1][0] + u[0] * basis[2][0])
    a.append(u[0] * basis[0][1] + u[1] * basis[1][1] + u[1] * basis[2][1])
    a.append(u[0] * basis[0][2] + u[2] * basis[1][2] + u[2] * basis[2][2])
    return a


stepb0 = map(u2a, atoms)
stepb1 = map(u2a, outcarIO.outcar2poscar(outcarFile, configRequest - 1)[2])
stepb2 = map(u2a, outcarIO.outcar2poscar(outcarFile, configRequest - 2)[2])
stepb3 = map(u2a, outcarIO.outcar2poscar(outcarFile, configRequest - 3)[2])
stepb4 = map(u2a, outcarIO.outcar2poscar(outcarFile, configRequest - 4)[2])

velo5 = list()
for b0, b1, b2, b3, b4 in zip(stepb0, stepb1, stepb2, stepb3, stepb4):
    velo5.append([
        (25 * b0[i] - 48 * b1[i] + 36 * b2[i] - 16 * b3[i] + 3 * b4[i]) /
        (12.0 * timestep) for i in range(3)
    ])

poscarIO.write("VDATCAR", basis, atoms, atypes, head, velocities=velo5)
Esempio n. 11
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    print "%s <lammps dump> <config #> <POSCAR output>" % sys.argv[0].split("/")[-1]
    print "If only the dump file is provided, the number of configurations will be reported"
    print "Converts a lammps dump to POSCAR"


# If only the filename is provided, count the number of configurations and spit that out
if len(sys.argv) == 2:
    dumpdata = open(sys.argv[1], "r").readlines()
    usage()
    print "\nNumber of configurations:", len([i for i in dumpdata if "ITEM: TIMESTEP" in i]), "\n"
    exit(0)

if len(sys.argv) != 4:
    usage()
    exit(0)

dumpdata = sys.argv[1]  # open(sys.argv[1],"r").readlines()
configN = int(sys.argv[2])
posname = sys.argv[3]

# Read in lammps data
basis, types, atoms = lammpsIO.readConfig(dumpdata, configN)

# atoms,types = zip(*[[[i[0],i[1],i[2]-basis[2][2]/2.0],t] for i,t in zip(atoms,types) if i[2]>basis[2][2]/2.0])
# basis[2][2]/=2.0

header = "POSCAR generated by %s on %s" % (sys.argv[0].split("/")[-1], time.asctime())
# Write out POSCAR data
atypes = [types.count(j) for j in sorted(list(set(types)))]
poscarIO.write(posname, basis, atoms, atypes, header, autoFrac=False, frac=False)
Esempio n. 12
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def prompt_iface(md,count,stresskb,T,PE,KE,ax,ay,az,afx,afy,afz,v1,v2,v3,types):
    print "="*50
    print "Step Number: %d"%(count)
    print "Stress (in kB) XX YY ZZ XY YZ XZ:"
    print stresskb
    if md==True:
        print "T=%g,   PE=%g,   TE=%g" % (T,PE,KE)
    else:
        print "PE=%g" % (PE)
    print "="*50
    print ""

    if not(plotdisabled):
        athread=threading.Thread(target=plot3,args=(md,ax,ay,az,afx,afy,afz,v1,v2,v3,types))
        athread.start()
        athread.join()
    while True:
        try:
            val=raw_input("Input coords and radius of sphere (x y z r) or (Enter) to continue:\n")
            [rx,ry,rz,rr]=[float(k) for k in val.split()]
            N=len(ax)
            atoms=[[ax[i],ay[i],az[i],types[i]] for i in range(N) if sqrt((ax[i]-rx)**2+(ay[i]-ry)**2+(az[i]-rz)**2)<=rr]
            atoms.sort(key=lambda x:x[3])
            d1,d2,d3,types=zip(*atoms)
            cs=[types.count(i) for i in range(max(types)+1)]

            while True:
                try:
                    val=float(raw_input("Scale factor (increases vacuum around cluster): \n"))
                except ValueError:
                    print "Scaling factor should be a floating point value between 1.2 and 3.0."
                else:
                    break

            for atom in atoms:
                print "% 5.5g  % 5.5g  % 5.5g" % (tuple(atom[:3]))

            poscarIO.write("POSCAR.CLUSTER%d"%len(atoms),array([v1,v2,v3])*val,[atom[:3] for atom in atoms],cs,"Cluster genearted by grabcluster.py")
            print "POSCAR.CLUSTER%d written to."%len(atoms) 
            exit(0)        

        except ValueError:
            if len(val)==0:
                break
        else:
            if not(plotdisabled):
                bthread=threading.Thread(target=plot3sphere,args=(md,ax,ay,az,afx,afy,afz,v1,v2,v3,rx,ry,rz,rr))
                bthread.start()
                bthread.join()
                try:
                    val=raw_input("Good? (y/n):")
                    if val=="y" or val=="Y":

                        N=len(ax)
                        atoms=[[ax[i],ay[i],az[i],types[i]] for i in range(N) if sqrt((ax[i]-rx)**2+(ay[i]-ry)**2+(az[i]-rz)**2)<=rr]

                        atoms.sort(key=lambda x:x[3])
                        d1,d2,d3,types=zip(*atoms)
                        cs=[types.count(i) for i in range(N)]
                        #cut off types list after last non-zero number
                        last=0
                        for i,v in enumerate(cs):
                            if v>0:
                                last=i
                        cs=cs[:last+1]
                        print cs[:]
                        for atom in atoms:
                            print "% 5.5g  % 5.5g  % 5.5g" % (tuple(atom[:3]))
                            
                        exit(0)
                except ValueError:
                    pass
Esempio n. 13
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def outcar2poscar(outcar, outposcar, wantconfig):
    basis, atypes, atoms, head, poscar = outcarIO.outcar2poscar(
        outcar, wantconfig)
    poscarIO.write(outposcar, basis, atoms, atypes, head)
Esempio n. 14
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    usage()
    print "\nNumber of configurations:", len(
        [i for i in dumpdata if "ITEM: TIMESTEP" in i]), "\n"
    exit(0)

if len(sys.argv) != 4:
    usage()
    exit(0)

dumpdata = sys.argv[1]  #open(sys.argv[1],"r").readlines()
configN = int(sys.argv[2])
posname = sys.argv[3]

#Read in lammps data
basis, types, atoms = lammpsIO.readConfig(dumpdata, configN)

#atoms,types = zip(*[[[i[0],i[1],i[2]-basis[2][2]/2.0],t] for i,t in zip(atoms,types) if i[2]>basis[2][2]/2.0])
#basis[2][2]/=2.0

header = "POSCAR generated by %s on %s" % (sys.argv[0].split("/")[-1],
                                           time.asctime())
#Write out POSCAR data
atypes = [types.count(j) for j in sorted(list(set(types)))]
poscarIO.write(posname,
               basis,
               atoms,
               atypes,
               header,
               autoFrac=False,
               frac=False)
Esempio n. 15
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if configRequest > nSteps:
    print "%d configurations available"%nSteps
    exit(0)
if configRequest < 5:
    print "Need more than 5 steps for backwards - finite difference method."
    exit(0)

#Gather poscar information for last set of atoms
basis,atypes,atoms,head,poscar = outcarIO.outcar2poscar(outcarFile,configRequest)

#Convert from fractional units to cartesian
def u2a(u):
    a=list()
    a.append(u[0]*basis[0][0]+u[0]*basis[1][0]+u[0]*basis[2][0])
    a.append(u[0]*basis[0][1]+u[1]*basis[1][1]+u[1]*basis[2][1])
    a.append(u[0]*basis[0][2]+u[2]*basis[1][2]+u[2]*basis[2][2])
    return a

stepb0 = map(u2a,atoms)
stepb1 = map(u2a,outcarIO.outcar2poscar(outcarFile,configRequest-1)[2])
stepb2 = map(u2a,outcarIO.outcar2poscar(outcarFile,configRequest-2)[2])
stepb3 = map(u2a,outcarIO.outcar2poscar(outcarFile,configRequest-3)[2])
stepb4 = map(u2a,outcarIO.outcar2poscar(outcarFile,configRequest-4)[2])

velo5=list()
for b0,b1,b2,b3,b4 in zip(stepb0,stepb1,stepb2,stepb3,stepb4):
    velo5.append( [(25*b0[i]-48*b1[i]+36*b2[i]-16*b3[i]+3*b4[i])/(12.0*timestep) for i in range(3)] )

poscarIO.write("VDATCAR",basis,atoms,atypes,head,velocities=velo5)