def gennewcoord(pbc):
#generate random vector on 1 sphere
orient = usefulmath.vec_random()
orient = usefulmath.vec_normalize(orient)
#generate position
pos = [random.random()*float(pbc[0]),random.random()*float(pbc[1]),random.random()*float(pbc[2])]
#generate patch (perpendicular to orientation of cylinder)
patch = usefulmath.perp_vec(orient)
patch = usefulmath.vec_normalize(patch)
#return [pos,orient]
return [pos,orient,patch]
def gennewcoord(pbc,dist):
#generate random vector on 1 sphere
orient=usefulmath.vec_random()
orient=usefulmath.vec_normalize(orient)
dist=float(dist);
dist2=2.0*dist;
#generate position
pos=[dist+random.random()*(float(pbc[0])-dist2),dist+random.random()*(float(pbc[1])-dist2),dist+random.random()*(float(pbc[2])-dist2)]
#generate patch (perpendicular to orientation of cylinder)
patch=usefulmath.perp_vec(orient)
patch=usefulmath.vec_normalize(patch)
#return [pos,orient]
return [pos,orient,patch]
def datatransform(data,leng,patch):
newdata=[]
for frame in data:
newframe=[]
for line in frame:
[x,y,z,vx,vy,vz,px,py,pz]=line[:]
vec=usefulmath.vec_normalize([vx,vy,vz])
newframe.append([x+leng/2*vec[0],y+leng/2*vec[1],z+leng/2*vec[2]])
newframe.append([x-leng/2*vec[0],y-leng/2*vec[1],z-leng/2*vec[2]])
newdata.append(newframe)
return newdata
def datatransform(data, leng, patch):
newdata = []
for frame in data:
newframe = []
for line in frame:
[x, y, z, vx, vy, vz, px, py, pz] = line[:]
vec = usefulmath.vec_normalize([vx, vy, vz])
newframe.append([
x + leng / 2 * vec[0], y + leng / 2 * vec[1],
z + leng / 2 * vec[2]
])
newframe.append([
x - leng / 2 * vec[0], y - leng / 2 * vec[1],
z - leng / 2 * vec[2]
])
newdata.append(newframe)
return newdata
def datatransform(data,leng,patch):
newdata=[]
for frame in data:
newframe=[]
for line in frame:
[x,y,z,vx,vy,vz,px,py,pz]=line[:]
vec=usefulmath.vec_normalize([vx,vy,vz])
newframe.append([x+leng/2*vec[0],y+leng/2*vec[1],z+leng/2*vec[2]])
newframe.append([x-leng/2*vec[0],y-leng/2*vec[1],z-leng/2*vec[2]])
patchmove=10*0.5*math.cos((patch+10)/2/180*math.pi)
newx=x+leng/2*vec[0]+patchmove*px
newy=y+leng/2*vec[1]+patchmove*py
newz=z+leng/2*vec[2]+patchmove*pz
newframe.append([newx,newy,newz])
newx=x-leng/2*vec[0]+patchmove*px
newy=y-leng/2*vec[1]+patchmove*py
newz=z-leng/2*vec[2]+patchmove*pz
newframe.append([newx,newy,newz])
newdata.append(newframe)
return newdata
def write_data(data,box,particles, types, geotypes, params,outfilename,outfilename2, switch, switchtypes, switchfile):
f = open(outfilename, 'w')
outstring=""
if (switch):
swstring=""
sf = open(switchfile, 'w')
#DEBUG
#print("Length of types")
#print(len(types))
#print("Len Data")
#print(len(data))
#print(types)
#print(geotypes)
for i in range(len(data)):
newline="CRYST1 %8.3f %8.3f %8.3f 90.00 90.00 90.00 P 1 1\n" % (box[i][0],box[i][1],box[i][2])
outstring=outstring+newline
frame=data[i]
#print("len frame")
#print(len(frame))
atm=1
for j in range(len(frame)):
[x,y,z,vx,vy,vz,px,py,pz,sw]=frame[j][:]
[x,y,z] = usefulmath.usepbc([x,y,z],box[i])
#if (types[j] <SP):
#print("j : %d\n" % j)
if (convert_geotype(geotypes[particles[j]]) <SP):
# Handle the switching
csw = 2 * sw + types[particles[j]] +0
psw = 2 * sw + types[particles[j]] +1
tsw = 2 * sw + types[particles[j]] +2
if (switch):
swstring = swstring + "%d %d %d %d " % (csw, csw, psw, psw)
vec=usefulmath.vec_normalize([vx,vy,vz])
#print head
leng = params[particles[j]][6]
nx=x+leng/2*vec[0]
ny=y+leng/2*vec[1]
nz=z+leng/2*vec[2]
#print("max j: %d; j: %d" % (len(frame), j))
newline="ATOM %5d C%1d PSC F%4d % 8.2f% 8.2f% 8.2f 1.00%6.2f\n" % (atm,particles[j],(j+1)%1000,nx,ny,nz,csw)
outstring=outstring+newline
atm=atm+1
#print tail
nx=x-leng/2*vec[0]
ny=y-leng/2*vec[1]
nz=z-leng/2*vec[2]
newline="ATOM %5d C%1d PSC F%4d % 8.2f% 8.2f% 8.2f 1.00%6.2f\n" % (atm,particles[j],(j+1)%1000,nx,ny,nz,csw)
outstring=outstring+newline
atm=atm+1
#print patch
#patch=params[types[j]][3]+2*params[types[j]][4]
patch=params[particles[j]][4]+2*params[particles[j]][5]
#print headpatch
patchmove=math.fabs(0.5*math.cos((patch+10*pow(patch/180,2))/360*math.pi)) # displacement
#patchmove= params[particles[j]][2] * patch/ 1080 + params[particles[j]][2] / 12 # displacement
# The displacement varries between sigma / 12 and sigma / 4 depending on the angle
nx=x+leng/2*vec[0]+patchmove*px
ny=y+leng/2*vec[1]+patchmove*py
nz=z+leng/2*vec[2]+patchmove*pz
newline="ATOM %5d P%1d PSC F%4d % 8.2f% 8.2f% 8.2f 1.00%6.2f\n" % (atm,particles[j],(j+1)%1000,nx,ny,nz,psw)
outstring=outstring+newline
atm=atm+1
#print tailpatch
nx=x-leng/2*vec[0]+patchmove*px
ny=y-leng/2*vec[1]+patchmove*py
nz=z-leng/2*vec[2]+patchmove*pz
newline="ATOM %5d P%1d PSC F%4d % 8.2f% 8.2f% 8.2f 1.00%6.2f\n" % (atm,particles[j],(j+1)%1000,nx,ny,nz,psw)
outstring=outstring+newline
atm=atm+1
if (convert_geotype(geotypes[particles[j]]) >=TPSC):
#print second patch
if (switch):
swstring = swstring + "%d %d " % (tsw, tsw)
vec2=[px,py,pz]
vec2=usefulmath.rotatevec(vec2,vec,params[particles[j]][7])
patch=params[particles[j]][8]+2*params[particles[j]][9]
#print headpatch
patchmove=0.5*math.cos((patch+10*pow(patch/180,2))/360*math.pi) # displacement
#patchmove= params[particles[j]][2] * patch/ 1080 + params[particles[j]][2] / 12 # displacement
# The displacement varries between sigma / 12 and sigma / 4 depending on the angle
nx=x+leng/2*vec[0]+patchmove*vec2[0]
ny=y+leng/2*vec[1]+patchmove*vec2[1]
nz=z+leng/2*vec[2]+patchmove*vec2[2]
newline="ATOM %5d T%1d PSC F%4d % 8.2f% 8.2f% 8.2f 1.00%6.2f\n" % (atm,particles[j],(j+1)%1000,nx,ny,nz,tsw)
outstring=outstring+newline
atm=atm+1
#print tailpatch
nx=x-leng/2*vec[0]+patchmove*vec2[0]
ny=y-leng/2*vec[1]+patchmove*vec2[1]
nz=z-leng/2*vec[2]+patchmove*vec2[2]
newline="ATOM %5d T%1d PSC F%4d % 8.2f% 8.2f% 8.2f 1.00%6.2f\n" % (atm,particles[j],(j+1)%1000,nx,ny,nz,tsw)
outstring=outstring+newline
atm=atm+1
else:
#print sphere
nx=x
ny=y
nz=z
newline="ATOM %5d S%1d PSC F%4d % 8.2f% 8.2f% 8.2f 1.00%6.2f\n" % (atm,particles[j]%SP,(j+1)%1000,nx,ny,nz,0)
atm=atm+1
outstring=outstring+newline
outstring=outstring+"END\n"
if (switch):
swstring = swstring + "\n"
f.write(outstring)
f.close()
if (switch):
sf.write(swstring)
sf.close()
return 0
