1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
|
c Create LAMMPS data file for collection of
c polymer bead-spring chains of various lengths and bead sizes
c Syntax: chain < def.chain > data.file
c def.chain is input file that specifies the chains
c data.file is output file that will be input for LAMMPS
c includes image flags in data file so chains can be unraveled later
program chain
integer swaptype
integer, allocatable :: nchain(:),nmonomer(:)
integer, allocatable :: ntype(:),nbondtype(:)
integer, allocatable :: type(:),molecule(:)
integer, allocatable :: imagex(:),imagey(:),imagez(:)
real*8, allocatable :: x(:),y(:),z(:)
real*8, allocatable :: bondlength(:),restrict(:)
common xprd,yprd,zprd,xboundlo,xboundhi,
$ yboundlo,yboundhi,zboundlo,zboundhi
real*8 random
900 format(a)
901 format(2f10.6,a)
902 format(i3,f5.1)
903 format(i10,i8,i8,3f10.4,3i4)
904 format(i6,i3,2i6)
c read chain definitions
read (5,*)
read (5,*)
read (5,*) rhostar
read (5,*) iseed
read (5,*) nsets
read (5,*) swaptype
allocate(nchain(nsets))
allocate(nmonomer(nsets))
allocate(ntype(nsets))
allocate(nbondtype(nsets))
allocate(bondlength(nsets))
allocate(restrict(nsets))
do iset = 1,nsets
read (5,*)
read (5,*) nchain(iset)
read (5,*) nmonomer(iset)
read (5,*) ntype(iset)
read (5,*) nbondtype(iset)
read (5,*) bondlength(iset)
read (5,*) restrict(iset)
enddo
c natoms = total # of monomers
natoms = 0
do iset = 1,nsets
natoms = natoms + nchain(iset)*nmonomer(iset)
enddo
allocate(x(natoms))
allocate(y(natoms))
allocate(z(natoms))
allocate(type(natoms))
allocate(molecule(natoms))
allocate(imagex(natoms))
allocate(imagey(natoms))
allocate(imagez(natoms))
c setup box size (sigma = 1.0)
volume = natoms/rhostar
xprd = volume**(1.0/3.0)
yprd = xprd
zprd = xprd
xboundlo = -xprd/2.0
xboundhi = -xboundlo
yboundlo = xboundlo
yboundhi = xboundhi
zboundlo = xboundlo
zboundhi = xboundhi
c generate random chains
c loop over sets and chains in each set
n = 0
nmolecule = 0
do iset = 1,nsets
do ichain = 1,nchain(iset)
nmolecule = nmolecule + 1
c random starting point for the chain in the box
x1 = 0.0
y1 = 0.0
z1 = 0.0
x2 = xboundlo + random(iseed)*xprd
y2 = yboundlo + random(iseed)*yprd
z2 = zboundlo + random(iseed)*zprd
c store 1st monomer of chain
c 1st monomer is always in original box (image = 0)
call pbc(x2,y2,z2)
n = n + 1
x(n) = x2
y(n) = y2
z(n) = z2
type(n) = ntype(iset)
imagex(n) = 0
imagey(n) = 0
imagez(n) = 0
if (swaptype == 0) then
molecule(n) = nmolecule
else
molecule(n) = 1
endif
c generate rest of monomers in this chain
do imonomer = 2,nmonomer(iset)
x0 = x1
y0 = y1
z0 = z1
x1 = x2
y1 = y2
z1 = z2
c random point inside sphere of unit radius
10 xinner = 2.0*random(iseed) - 1.0
yinner = 2.0*random(iseed) - 1.0
zinner = 2.0*random(iseed) - 1.0
rsq = xinner*xinner + yinner*yinner + zinner*zinner
if (rsq > 1.0) goto 10
c project point to surface of sphere of unit radius
r = sqrt(rsq)
xsurf = xinner/r
ysurf = yinner/r
zsurf = zinner/r
c create new point by scaling unit offsets by bondlength (sigma = 1.0)
x2 = x1 + xsurf*bondlength(iset)
y2 = y1 + ysurf*bondlength(iset)
z2 = z1 + zsurf*bondlength(iset)
c check that new point meets restriction requirement
c only for 3rd monomer and beyond
dx = x2 - x0
dy = y2 - y0
dz = z2 - z0
r = sqrt(dx*dx + dy*dy + dz*dz)
if (imonomer > 2 .and. r <= restrict(iset)) goto 10
c store new point
c if delta to previous bead is large, then increment/decrement image flag
call pbc(x2,y2,z2)
n = n + 1
x(n) = x2
y(n) = y2
z(n) = z2
type(n) = ntype(iset)
if (abs(x(n)-x(n-1)) < 2.0*bondlength(iset)) then
imagex(n) = imagex(n-1)
else if (x(n) - x(n-1) < 0.0) then
imagex(n) = imagex(n-1) + 1
else if (x(n) - x(n-1) > 0.0) then
imagex(n) = imagex(n-1) - 1
endif
if (abs(y(n)-y(n-1)) < 2.0*bondlength(iset)) then
imagey(n) = imagey(n-1)
else if (y(n) - y(n-1) < 0.0) then
imagey(n) = imagey(n-1) + 1
else if (y(n) - y(n-1) > 0.0) then
imagey(n) = imagey(n-1) - 1
endif
if (abs(z(n)-z(n-1)) < 2.0*bondlength(iset)) then
imagez(n) = imagez(n-1)
else if (z(n) - z(n-1) < 0.0) then
imagez(n) = imagez(n-1) + 1
else if (z(n) - z(n-1) > 0.0) then
imagez(n) = imagez(n-1) - 1
endif
if (swaptype == 0) then
molecule(n) = nmolecule
else if (swaptype == 1) then
molecule(n) = imonomer
else if (swaptype == 2) then
if (imonomer <= nmonomer(iset)/2) then
molecule(n) = imonomer
else
molecule(n) = nmonomer(iset)+1-imonomer
endif
endif
enddo
enddo
enddo
c compute quantities needed for LAMMPS file
nbonds = 0
ntypes = 0
nbondtypes = 0
do iset = 1,nsets
nbonds = nbonds + nchain(iset)*(nmonomer(iset)-1)
if (ntype(iset) > ntypes) ntypes = ntype(iset)
if (nbondtype(iset) > nbondtypes)
$ nbondtypes = nbondtype(iset)
enddo
c write out LAMMPS file
write (6,900) 'LAMMPS FENE chain data file'
write (6,*)
write (6,*) natoms,' atoms'
write (6,*) nbonds,' bonds'
write (6,*) 0,' angles'
write (6,*) 0,' dihedrals'
write (6,*) 0,' impropers'
write (6,*)
write (6,*) ntypes,' atom types'
write (6,*) nbondtypes,' bond types'
write (6,*) 0,' angle types'
write (6,*) 0,' dihedral types'
write (6,*) 0,' improper types'
write (6,*)
write (6,901) xboundlo,xboundhi,' xlo xhi'
write (6,901) yboundlo,yboundhi,' ylo yhi'
write (6,901) zboundlo,zboundhi,' zlo zhi'
write (6,*)
write (6,900) 'Masses'
write (6,*)
do i = 1,ntypes
write (6,902) i,1.0
enddo
write (6,*)
write (6,900) 'Atoms'
write (6,*)
do i = 1,natoms
write (6,903) i,molecule(i),type(i),x(i),y(i),z(i),
$ imagex(i),imagey(i),imagez(i)
enddo
if (nbonds > 0) then
write (6,*)
write (6,900) 'Bonds'
write (6,*)
n = 0
m = 0
do iset = 1,nsets
do ichain = 1,nchain(iset)
do imonomer = 1,nmonomer(iset)
n = n + 1
if (imonomer /= nmonomer(iset)) then
m = m + 1
write (6,904) m,nbondtype(iset),n,n+1
endif
enddo
enddo
enddo
endif
end
c ************
c Subroutines
c ************
c periodic boundary conditions - map atom back into periodic box
subroutine pbc(x,y,z)
common xprd,yprd,zprd,xboundlo,xboundhi,
$ yboundlo,yboundhi,zboundlo,zboundhi
if (x < xboundlo) x = x + xprd
if (x >= xboundhi) x = x - xprd
if (y < yboundlo) y = y + yprd
if (y >= yboundhi) y = y - yprd
if (z < zboundlo) z = z + zprd
if (z >= zboundhi) z = z - zprd
return
end
c RNG from Numerical Recipes
real*8 function random(iseed)
real*8 aa,mm,sseed
parameter (aa=16807.0D0,mm=2147483647.0D0)
sseed = iseed
sseed = mod(aa*sseed,mm)
random = sseed/mm
iseed = sseed
return
end
|
