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
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
|
c -------------------------------------------------------------------------
c Code converts LAMMPS atom dumps to CHARMM .dcd files
c Paul Crozier, SNL, 2003
c -------------------------------------------------------------------------
c -------------------------------------------------------------------------
program mkdcd
parameter (max_atoms = 100000)
common/int_variables/ n_con_files, n_con_files_to_skip,
1 n_frames_per_con_file, n_frames_per_dump_to_dcd,
2 max_dcd_dumps_per_dcd_file, n_dcd_files_to_skip, n_frames,
3 n_frames_to_skip, ith_frame, ith_dump_to_dcd, n_timesteps,
4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter,
5 i_recenter_flag
common/real_variables/ xprd, yprd, zprd, box(2,3),
1 x(3,max_atoms)
common/char_variables/ con_file_path, dcd_file_path
character*76 con_file_path
character*76 dcd_file_path
call read_in_mkdcd
do ith_frame = n_frames_to_skip+1, n_frames
call find_config
call read_config
if (i_recenter_flag == 1) call recenter
if (mod(ith_frame,n_frames_per_dump_to_dcd) == 0) call mk_dcd
enddo
write(6,*) 'Done.'
stop
end
c -------------------------------------------------------------------------
subroutine find_config
parameter (max_atoms = 100000)
common/int_variables/ n_con_files, n_con_files_to_skip,
1 n_frames_per_con_file, n_frames_per_dump_to_dcd,
2 max_dcd_dumps_per_dcd_file, n_dcd_files_to_skip, n_frames,
3 n_frames_to_skip, ith_frame, ith_dump_to_dcd, n_timesteps,
4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter,
5 i_recenter_flag
common/real_variables/ xprd, yprd, zprd, box(2,3),
1 x(3,max_atoms)
common/char_variables/ con_file_path, dcd_file_path
character*76 con_file_path
character*76 dcd_file_path
integer l,m,n,i,j,itag
real*8 buf(8)
if (mod((ith_frame-1),n_frames_per_con_file) == 0) then
n = (ith_frame-1)/n_frames_per_con_file + 1
write(6,*) 'On config file # ', n
close(21)
if (n < 10) then
open(21,file="conf"//char(48+n),status='old')
elseif (n < 100) then
m = n/10
n = mod(n,10)
open(21,file="conf"
$ //char(48+m)//char(48+n),status='old')
else
l = n/100
m = (n - 100*l)/10
n = mod(n,10)
open(21,file="conf"
$ //char(48+l)//char(48+m)//char(48+n),status='old')
endif
rewind 21
c skip the first frame of each config file
read(21,*)
read(21,*) n_timesteps
read(21,*)
read(21,*) n_atoms
read(21,*)
read(21,*) box(1,1),box(2,1)
read(21,*) box(1,2),box(2,2)
read(21,*) box(1,3),box(2,3)
read(21,*)
xprd = box(2,1) - box(1,1)
yprd = box(2,2) - box(1,2)
zprd = box(2,3) - box(1,3)
if (n_atoms > max_atoms) write(6,*) "n_atoms > max_atoms"
n_frozen_atoms = 1000000000
do i = 1, n_atoms
read (21,*) (buf(j),j=1,5)
itag = nint(buf(1))
n_frozen_atoms = min(itag,n_frozen_atoms)
enddo
n_frozen_atoms = n_frozen_atoms - 1
i_recenter_flag = 0
if (n_atoms_recenter < n_atoms) i_recenter_flag = 1
endif
return
end
c -------------------------------------------------------------------------
subroutine mk_dcd
parameter (max_atoms = 100000)
common/int_variables/ n_con_files, n_con_files_to_skip,
1 n_frames_per_con_file, n_frames_per_dump_to_dcd,
2 max_dcd_dumps_per_dcd_file, n_dcd_files_to_skip, n_frames,
3 n_frames_to_skip, ith_frame, ith_dump_to_dcd, n_timesteps,
4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter,
5 i_recenter_flag
common/real_variables/ xprd, yprd, zprd, box(2,3),
1 x(3,max_atoms)
common/char_variables/ con_file_path, dcd_file_path
character*76 con_file_path
character*76 dcd_file_path
real*8 xtlabc(6)
integer i
if (mod(ith_dump_to_dcd,max_dcd_dumps_per_dcd_file) == 0)
& call mk_dcd_start
ith_dump_to_dcd = ith_dump_to_dcd + 1
write(6,*) 'Frame # ', ith_frame,
& ', Dump to .dcd #', ith_dump_to_dcd
xtlabc(1) = xprd
xtlabc(2) = 0.0
xtlabc(3) = yprd
xtlabc(4) = 0.0
xtlabc(5) = 0.0
xtlabc(6) = zprd
write(26) xtlabc
write(26) (x(1,i), i=1,n_atoms_dump)
write(26) (x(2,i), i=1,n_atoms_dump)
write(26) (x(3,i), i=1,n_atoms_dump)
return
end
c -------------------------------------------------------------------------
subroutine mk_dcd_start
parameter (max_atoms = 100000)
common/int_variables/ n_con_files, n_con_files_to_skip,
1 n_frames_per_con_file, n_frames_per_dump_to_dcd,
2 max_dcd_dumps_per_dcd_file, n_dcd_files_to_skip, n_frames,
3 n_frames_to_skip, ith_frame, ith_dump_to_dcd, n_timesteps,
4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter,
5 i_recenter_flag
common/real_variables/ xprd, yprd, zprd, box(2,3),
1 x(3,max_atoms)
common/char_variables/ con_file_path, dcd_file_path
character*76 con_file_path
character*76 dcd_file_path
character*4 hdr
integer icntrl(20), nstr, n_dcd_file, n, m
write(6,*) 'Creating new .dcd file . . . '
n_dcd_file = ith_dump_to_dcd/max_dcd_dumps_per_dcd_file +
& n_dcd_files_to_skip + 1
m = n_dcd_file/10
n = mod(n_dcd_file,10)
close(26)
open(26,file="out"
$ //char(48+m)//char(48+n)//'.dcd',form='unformatted')
hdr = 'CORD'
do n = 1,20
icntrl(n) = 0
enddo
nstr = 0 ! number of strings in header
icntrl(1) = max_dcd_dumps_per_dcd_file ! number of frames in traj file
icntrl(2) = 1 ! number of steps in previous run
icntrl(3) = 1 ! frequency of saving
icntrl(4) = max_dcd_dumps_per_dcd_file ! total number of steps
icntrl(8) = n_atoms_dump*3 - 6 ! number of degrees of freedom
icntrl(10) = 981668463 ! coded time step
icntrl(11) = 1 ! coded crystallographic group (or zero)
icntrl(20) = 28 ! CHARMM version number
write(26) hdr, icntrl
write(26) nstr
write(26) n_atoms_dump
return
end
c -------------------------------------------------------------------------
c input data from config file
subroutine read_config
parameter (max_atoms = 100000)
common/int_variables/ n_con_files, n_con_files_to_skip,
1 n_frames_per_con_file, n_frames_per_dump_to_dcd,
2 max_dcd_dumps_per_dcd_file, n_dcd_files_to_skip, n_frames,
3 n_frames_to_skip, ith_frame, ith_dump_to_dcd, n_timesteps,
4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter,
5 i_recenter_flag
common/real_variables/ xprd, yprd, zprd, box(2,3),
1 x(3,max_atoms)
common/char_variables/ con_file_path, dcd_file_path
character*76 con_file_path
character*76 dcd_file_path
c local variables
integer i,j,itag,itrue
real*8 buf(8)
read(21,*)
read(21,*) n_timesteps
read(21,*)
read(21,*) n_atoms
read(21,*)
read(21,*) box(1,1),box(2,1)
read(21,*) box(1,2),box(2,2)
read(21,*) box(1,3),box(2,3)
read(21,*)
xprd = box(2,1) - box(1,1)
yprd = box(2,2) - box(1,2)
zprd = box(2,3) - box(1,3)
do i = 1, n_atoms
read (21,*) (buf(j),j=1,5)
c itag = nint(buf(1)) - n_frozen_atoms
c x(1,itag) = buf(3)*xprd + box(1,1)
c x(2,itag) = buf(4)*yprd + box(1,2)
c x(3,itag) = buf(5)*zprd + box(1,3)
x(1,i) = buf(3)*xprd + box(1,1)
x(2,i) = buf(4)*yprd + box(1,2)
x(3,i) = buf(5)*zprd + box(1,3)
enddo
return
end
c -------------------------------------------------------------------------
c read data from in_mkdcd file
subroutine read_in_mkdcd
parameter (max_atoms = 100000)
common/int_variables/ n_con_files, n_con_files_to_skip,
1 n_frames_per_con_file, n_frames_per_dump_to_dcd,
2 max_dcd_dumps_per_dcd_file, n_dcd_files_to_skip, n_frames,
3 n_frames_to_skip, ith_frame, ith_dump_to_dcd, n_timesteps,
4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter,
5 i_recenter_flag
common/real_variables/ xprd, yprd, zprd, box(2,3),
1 x(3,max_atoms)
common/char_variables/ con_file_path, dcd_file_path
character*76 con_file_path
character*76 dcd_file_path
100 format (a)
open(22,file='in_mkdcd')
rewind 22
read (22,*) n_con_files
read (22,*) n_con_files_to_skip
read (22,*) n_frames_per_con_file
read (22,*) n_frames_per_dump_to_dcd
read (22,*) max_dcd_dumps_per_dcd_file
read (22,*) n_dcd_files_to_skip
read (22,*) n_atoms_dump
read (22,*) n_atoms_recenter
read (22,100) con_file_path
read (22,100) dcd_file_path
n_frames = n_con_files * n_frames_per_con_file
n_frames_to_skip = n_con_files_to_skip * n_frames_per_con_file
ith_frame = n_frames_to_skip
ith_dump_to_dcd = 0
close (22)
return
end
c -------------------------------------------------------------------------
c recenter box on the average position of the first n_atoms_recenter atoms
subroutine recenter
parameter (max_atoms = 100000)
common/int_variables/ n_con_files, n_con_files_to_skip,
1 n_frames_per_con_file, n_frames_per_dump_to_dcd,
2 max_dcd_dumps_per_dcd_file, n_dcd_files_to_skip, n_frames,
3 n_frames_to_skip, ith_frame, ith_dump_to_dcd, n_timesteps,
4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter,
5 i_recenter_flag
common/real_variables/ xprd, yprd, zprd, box(2,3),
1 x(3,max_atoms)
common/char_variables/ con_file_path, dcd_file_path
character*76 con_file_path
character*76 dcd_file_path
integer i
real*8 ave_x, ave_y, ave_z
ave_x = 0.0
ave_y = 0.0
ave_z = 0.0
do i = 1, n_atoms_recenter
ave_x = ave_x + x(1,i)
ave_y = ave_y + x(2,i)
ave_z = ave_z + x(3,i)
enddo
ave_x = ave_x/float(n_atoms_recenter)
ave_y = ave_y/float(n_atoms_recenter)
ave_z = ave_z/float(n_atoms_recenter)
do i = 1, n_atoms_dump
x(1,i) = x(1,i) - ave_x
x(2,i) = x(2,i) - ave_y
x(3,i) = x(3,i) - ave_z
enddo
do i = 1, n_atoms_dump
x(1,i) = x(1,i) - xprd*(nint(x(1,i)/xprd))
x(2,i) = x(2,i) - xprd*(nint(x(2,i)/yprd))
x(3,i) = x(3,i) - xprd*(nint(x(3,i)/zprd))
enddo
return
end
c -------------------------------------------------------------------------
|
