| 1 |
module xyz_io |
| 2 |
use definitions, ONLY : DP,machdep_lnblnk,machdep_flush |
| 3 |
use parameter |
| 4 |
use simulation |
| 5 |
use model_module |
| 6 |
use status |
| 7 |
use file_units, ONLY : next_unit |
| 8 |
#ifdef MPI |
| 9 |
use mpi_module |
| 10 |
#endif |
| 11 |
implicit none |
| 12 |
PRIVATE |
| 13 |
|
| 14 |
|
| 15 |
!various common formats |
| 16 |
character(len=*), parameter :: xyz_line1 = "(i11)" |
| 17 |
character(len=*), parameter :: xyz_line2 = "(i11,3es12.3)" |
| 18 |
character(len=*), parameter :: xyz_coord = "(a3,6es12.3,i3)" |
| 19 |
|
| 20 |
|
| 21 |
|
| 22 |
! atype interface |
| 23 |
character(len=2) :: charident |
| 24 |
character(len=2) :: atid |
| 25 |
|
| 26 |
integer :: dump_unit |
| 27 |
integer :: eor_unit |
| 28 |
integer :: force_unit |
| 29 |
|
| 30 |
#ifdef MPI |
| 31 |
integer, dimension(mpi_status_size) :: istatus |
| 32 |
#endif |
| 33 |
|
| 34 |
public :: open_xyz_files |
| 35 |
public :: read_initial_config |
| 36 |
public :: dump_config |
| 37 |
public :: write_final_config |
| 38 |
public :: dump_forces |
| 39 |
#ifdef MPI |
| 40 |
public :: mpi_dump_q |
| 41 |
#endif |
| 42 |
|
| 43 |
|
| 44 |
contains |
| 45 |
|
| 46 |
!! open input and output files for simulation |
| 47 |
subroutine open_xyz_files(this_error) |
| 48 |
character(len=80) :: dump_file, msg |
| 49 |
character(len=80) :: force_file |
| 50 |
character(len=*), parameter :: routine_name = "OPEN_FILES" |
| 51 |
integer, optional :: this_error |
| 52 |
integer :: err |
| 53 |
#ifndef MPI |
| 54 |
integer, parameter :: node = 0 |
| 55 |
#endif |
| 56 |
|
| 57 |
if (present(this_error)) this_error = 0 |
| 58 |
|
| 59 |
if (node == 0) then |
| 60 |
|
| 61 |
dump_unit = next_unit() |
| 62 |
|
| 63 |
dump_file = file_prefix(1:machdep_lnblnk(file_prefix)) // '.dump' |
| 64 |
open(file=dump_file, unit=dump_unit, status='replace', iostat=err, & |
| 65 |
action='write') |
| 66 |
if (err > 0) then |
| 67 |
write(msg,*) "Error opening dump file", trim(dump_file) |
| 68 |
call info(routine_name, msg) |
| 69 |
if (present(this_error)) this_error = -1 |
| 70 |
end if |
| 71 |
write(msg,*) 'configurations will dump to: ', trim(dump_file) |
| 72 |
call info(routine_name, msg) |
| 73 |
|
| 74 |
|
| 75 |
|
| 76 |
!!$ force_file = file_prefix(1:machdep_lnblnk(file_prefix)) // '.force' |
| 77 |
!!$ open(file=force_file, unit=force_unit, status='replace', iostat= err, & |
| 78 |
!!$ action='write') |
| 79 |
!!$ |
| 80 |
!!$ if (err > 0) then |
| 81 |
!!$ write(msg,*) "Error opening force file", trim(force_file) |
| 82 |
!!$ call info(routine_name, msg) |
| 83 |
!!$ end if |
| 84 |
!!$ write(msg,*) 'Force dump will be in: ', trim(force_file) |
| 85 |
!!$ call info(routine_name, msg) |
| 86 |
|
| 87 |
end if |
| 88 |
end subroutine open_xyz_files |
| 89 |
|
| 90 |
|
| 91 |
|
| 92 |
subroutine read_initial_config(this_error) |
| 93 |
! Reads In the current configuration in XYZ file format. The next |
| 94 |
! frame in XYZ is simply appended to the end of the current frame. |
| 95 |
|
| 96 |
!standard io |
| 97 |
integer :: fu, i, a, atom, nats, id, junk,j |
| 98 |
integer :: natoms_tmp, id_tmp |
| 99 |
integer, intent(out), optional :: this_error |
| 100 |
character(len=2), allocatable, dimension(:) :: atid_tmp, atid_array |
| 101 |
character(len=120) :: msg |
| 102 |
integer :: read_error |
| 103 |
integer :: xyz_input_unit |
| 104 |
integer :: err |
| 105 |
character(len=80) :: input_file |
| 106 |
|
| 107 |
!mpi stuff |
| 108 |
integer :: iproc, ncount |
| 109 |
#ifndef MPI |
| 110 |
integer,parameter :: node = 0 |
| 111 |
#endif |
| 112 |
|
| 113 |
natoms_tmp = 0 |
| 114 |
|
| 115 |
if (present(this_error)) this_error = 0 |
| 116 |
|
| 117 |
call info("READ_INITIAL_CONFIG","Reading old trajectory file") |
| 118 |
#ifdef MPI |
| 119 |
if (node == 0) then |
| 120 |
#endif |
| 121 |
input_file = file_prefix(1:machdep_lnblnk(file_prefix)) // '.in' |
| 122 |
xyz_input_unit = next_unit() |
| 123 |
open(file=input_file, unit=xyz_input_unit, status='old',iostat=err, & |
| 124 |
action='read') |
| 125 |
if (err > 0 ) then |
| 126 |
write(msg,*) "Error opening config file", trim(input_file) |
| 127 |
call info("READ_INITIAL_CONFIG", msg) |
| 128 |
if (present(this_error)) this_error = -1 |
| 129 |
end if |
| 130 |
|
| 131 |
write(msg,*) 'reading initial config from: ', trim(input_file) |
| 132 |
call info("READ_INITIAL_CONFIG", msg) |
| 133 |
#ifdef MPI |
| 134 |
endif |
| 135 |
#endif |
| 136 |
|
| 137 |
|
| 138 |
#ifndef MPI |
| 139 |
|
| 140 |
read(unit=xyz_input_unit,fmt=*,iostat=read_error) natoms_tmp |
| 141 |
read(xyz_input_unit,*) |
| 142 |
|
| 143 |
if (read_error /= 0) then |
| 144 |
write(msg,*) "Error reading particle configuration: ", i, "Atom: ",atom |
| 145 |
call info("READ_INITIAL_CONFIG",msg) |
| 146 |
if (present(this_error)) this_error = -1 |
| 147 |
return |
| 148 |
else if (natoms /= natoms_tmp) then |
| 149 |
write(msg,*) 'Atom number mismatch read: ',natoms_tmp, & |
| 150 |
'Allocated: ', natoms |
| 151 |
call info('READ_INITIAL_CONFIG', msg) |
| 152 |
if (present(this_error)) this_error = -1 |
| 153 |
return |
| 154 |
end if |
| 155 |
|
| 156 |
|
| 157 |
|
| 158 |
! this block is only true for monatomic systems |
| 159 |
!! fix me for general case |
| 160 |
nmol = natoms |
| 161 |
do i = 1, nmol |
| 162 |
na(i) = 1 |
| 163 |
atom_index(i,1) = i |
| 164 |
enddo |
| 165 |
|
| 166 |
do i = 1, nmol |
| 167 |
do a = 1, na(i) |
| 168 |
atom = atom_index(i,a) |
| 169 |
read(unit=xyz_input_unit,fmt=*,iostat=read_error) atid, q(1,atom), q(2,atom), q(3,atom), & |
| 170 |
v(1,atom), v(2,atom), v(3,atom) |
| 171 |
if (read_error /= 0) then |
| 172 |
write(msg,*) "Error reading particle configuration: ", i, "Atom: ",atom |
| 173 |
call info("READ_INITIAL_CONFIG",msg) |
| 174 |
if (present(this_error)) this_error = -1 |
| 175 |
return |
| 176 |
end if |
| 177 |
id = atype_atoi(atid) |
| 178 |
ident(atom) = id |
| 179 |
! this line only works for monatomic systems: |
| 180 |
model(i) = atype_identifier(id) |
| 181 |
mass(atom) = atype_mass(id) |
| 182 |
end do |
| 183 |
end do |
| 184 |
|
| 185 |
#else |
| 186 |
if (node == 0) then |
| 187 |
allocate(atid_tmp(max_local)) |
| 188 |
else |
| 189 |
allocate(atid_array(max_local)) |
| 190 |
end if |
| 191 |
|
| 192 |
|
| 193 |
if (node == 0) then |
| 194 |
read(xyz_input_unit,*) natoms_tmp |
| 195 |
read(xyz_input_unit,*) |
| 196 |
end if |
| 197 |
|
| 198 |
call mpi_bcast(natoms_tmp,1,mpi_integer,0,mpi_comm_world,mpi_err) |
| 199 |
if (mpi_err /= 0) then |
| 200 |
call error("READ_INITIAL_CONFIG","Error bcast natoms_tmp") |
| 201 |
endif |
| 202 |
|
| 203 |
if (natoms_tmp /= natoms) then |
| 204 |
write(msg,*) 'Atom number mismatch read: ',natoms_tmp, & |
| 205 |
'Allocated: ', natoms |
| 206 |
call error('READ_INITIAL_CONFIG', msg) |
| 207 |
end if |
| 208 |
|
| 209 |
call mpi_bcast(natoms,1,mpi_integer,0,mpi_comm_world,mpi_err) |
| 210 |
if (mpi_err /= 0) then |
| 211 |
call error("READ_INITIAL_CONFIG","Error bcast natoms") |
| 212 |
endif |
| 213 |
|
| 214 |
! this block is only true for monatomic systems |
| 215 |
nmol = natoms |
| 216 |
|
| 217 |
do i = 1, maxmol_local |
| 218 |
na(i) = 1 |
| 219 |
atom_index(i,1) = i |
| 220 |
end do |
| 221 |
|
| 222 |
if (node == 0) then |
| 223 |
do iproc = 0, nprocs - 1 |
| 224 |
|
| 225 |
ncount = nint(float(iproc+1)/nprocs*nmol) - & |
| 226 |
nint(float(iproc)/nprocs*nmol) |
| 227 |
do i = 1,ncount |
| 228 |
do a = 1, na(i) |
| 229 |
atom = atom_index(i,a) |
| 230 |
read(xyz_input_unit,*) atid_tmp(i), q_tmp(1,atom), q_tmp(2,atom), & |
| 231 |
q_tmp(3,atom), & |
| 232 |
v_tmp(1,atom), v_tmp(2,atom), v_tmp(3,atom) |
| 233 |
end do |
| 234 |
end do |
| 235 |
|
| 236 |
if (iproc.eq.0) then |
| 237 |
do i = 1,ncount |
| 238 |
do a = 1, na(i) |
| 239 |
atom = atom_index(i,a) |
| 240 |
q(1,atom) = q_tmp(1,atom) |
| 241 |
q(2,atom) = q_tmp(2,atom) |
| 242 |
q(3,atom) = q_tmp(3,atom) |
| 243 |
v(1,atom) = v_tmp(1,atom) |
| 244 |
v(2,atom) = v_tmp(2,atom) |
| 245 |
v(3,atom) = v_tmp(3,atom) |
| 246 |
id = atype_atoi(atid_tmp(i)) |
| 247 |
ident(atom) = id |
| 248 |
! this line only works for monatomic systems: |
| 249 |
model(i) = atype_identifier(id) |
| 250 |
mass(atom) = atype_mass(id) |
| 251 |
end do |
| 252 |
enddo |
| 253 |
else |
| 254 |
|
| 255 |
call mpi_send(atid_tmp,2*ncount,mpi_character,iproc,0, & |
| 256 |
mpi_comm_world,mpi_err) |
| 257 |
if (mpi_err /= 0) then |
| 258 |
call error("READ_INITIAL_CONFIG","Error mpi_send atid_tmp") |
| 259 |
endif |
| 260 |
call mpi_send(q_tmp,3*ncount,mpi_double_precision, & |
| 261 |
iproc,0,mpi_comm_world,mpi_err) |
| 262 |
if (mpi_err /= 0) then |
| 263 |
call error("READ_INITIAL_CONFIG","Error mpi_send q_tmp") |
| 264 |
endif |
| 265 |
call mpi_send(v_tmp,3*ncount,mpi_double_precision, & |
| 266 |
iproc,0,mpi_comm_world,mpi_err) |
| 267 |
if (mpi_err /= 0) then |
| 268 |
call error("READ_INITIAL_CONFIG","Error mpi_send v_tmp") |
| 269 |
endif |
| 270 |
|
| 271 |
endif |
| 272 |
|
| 273 |
end do |
| 274 |
close(xyz_input_unit) |
| 275 |
else |
| 276 |
call mpi_recv(atid_array,2*max_local,mpi_character,0,0, & |
| 277 |
mpi_comm_world,istatus,mpi_err) |
| 278 |
if (mpi_err /= 0) then |
| 279 |
call error("READ_INITIAL_CONFIG","Error reading atid_array") |
| 280 |
endif |
| 281 |
call mpi_recv(q,3*max_local, & |
| 282 |
mpi_double_precision,0,0,mpi_comm_world,istatus,mpi_err) |
| 283 |
if (mpi_err /= 0) then |
| 284 |
call error("READ_INITIAL_CONFIG","Error reading q_array") |
| 285 |
endif |
| 286 |
call mpi_recv(v,3*max_local, & |
| 287 |
mpi_double_precision,0,0,mpi_comm_world,istatus,mpi_err) |
| 288 |
if (mpi_err /= 0) then |
| 289 |
call error("READ_INITIAL_CONFIG","Error reading v_array") |
| 290 |
endif |
| 291 |
|
| 292 |
do j = 1,nlocal |
| 293 |
! array error here..... |
| 294 |
id = atype_atoi(atid_array(j)) |
| 295 |
ident(j) = id |
| 296 |
! this line only works for monatomic systems: |
| 297 |
model(j) = atype_identifier(id) |
| 298 |
mass(j) = atype_mass(id) |
| 299 |
end do |
| 300 |
|
| 301 |
end if |
| 302 |
call mpi_barrier(mpi_comm_world,mpi_err) |
| 303 |
|
| 304 |
|
| 305 |
|
| 306 |
if (node == 0) then |
| 307 |
deallocate(atid_tmp) |
| 308 |
close(xyz_input_unit) |
| 309 |
else |
| 310 |
deallocate(atid_array) |
| 311 |
end if |
| 312 |
#endif |
| 313 |
end subroutine read_initial_config |
| 314 |
|
| 315 |
subroutine dump_config(time) |
| 316 |
include 'headers/atom.h' |
| 317 |
|
| 318 |
real(kind=DP), intent(in) :: time |
| 319 |
#ifdef MPI |
| 320 |
integer, dimension(maxmol_local) :: na_tmp |
| 321 |
integer, dimension(maxmol_local,3) :: atom_index_tmp |
| 322 |
integer, dimension(max_local) :: ident_tmp |
| 323 |
#endif |
| 324 |
integer ::i,j, iproc, a |
| 325 |
integer :: atom |
| 326 |
integer :: icnt, i_a_cnt |
| 327 |
character(len=10) :: chartmp |
| 328 |
|
| 329 |
#ifndef MPI |
| 330 |
write(dump_unit,*) natoms |
| 331 |
write(dump_unit,*) time |
| 332 |
|
| 333 |
do i = 1, natoms |
| 334 |
charident = atype_identifier(ident(i)) // ' ' |
| 335 |
write(unit=dump_unit,fmt=xyz_coord) charident, (q(j,i),j=1,3), & |
| 336 |
(v(j,i),j=1,3), ident(i) |
| 337 |
end do |
| 338 |
|
| 339 |
call machdep_flush(dump_unit) |
| 340 |
#else |
| 341 |
if (node /= 0) then |
| 342 |
call mpi_send(na,nmol_local,mpi_integer,0,0, & |
| 343 |
mpi_comm_world,mpi_err) |
| 344 |
if (mpi_err /= 0) then |
| 345 |
call error("DUMP_CONFIG","Error sending na") |
| 346 |
endif |
| 347 |
call mpi_send(atom_index,3*nmol_local,mpi_integer,0,0, & |
| 348 |
mpi_comm_world,mpi_err) |
| 349 |
if (mpi_err /= 0) then |
| 350 |
call error("DUMP_CONFIG","Error sending atom_index") |
| 351 |
endif |
| 352 |
call mpi_send(ident,nlocal,mpi_integer,0,0, & |
| 353 |
mpi_comm_world,mpi_err) |
| 354 |
if (mpi_err /= 0) then |
| 355 |
call error("DUMP_CONFIG","Error sending ident") |
| 356 |
endif |
| 357 |
call mpi_send(q,3*nlocal,mpi_double_precision,0,0, & |
| 358 |
mpi_comm_world,mpi_err) |
| 359 |
if (mpi_err /= 0) then |
| 360 |
call error("DUMP_CONFIG","Error sending q") |
| 361 |
endif |
| 362 |
call mpi_send(v,3*nlocal,mpi_double_precision,0,0, & |
| 363 |
mpi_comm_world,mpi_err) |
| 364 |
if (mpi_err /= 0) then |
| 365 |
call error("DUMP_CONFIG","Error sending v") |
| 366 |
endif |
| 367 |
|
| 368 |
else |
| 369 |
|
| 370 |
|
| 371 |
write(dump_unit,*) natoms |
| 372 |
write(dump_unit,*) time |
| 373 |
|
| 374 |
|
| 375 |
do i = 1, nlocal |
| 376 |
charident = atype_identifier(ident(i)) // ' ' |
| 377 |
write(unit=dump_unit,fmt=xyz_coord) charident, (q(j,i),j=1,3), & |
| 378 |
(v(j,i),j=1,3), ident(i) |
| 379 |
end do |
| 380 |
|
| 381 |
do iproc = 1,nprocs - 1 |
| 382 |
icnt = 0 |
| 383 |
call mpi_recv(na_tmp, maxmol_local, mpi_integer,iproc,0, & |
| 384 |
mpi_comm_world,istatus,mpi_err) |
| 385 |
|
| 386 |
call mpi_get_count(istatus,mpi_integer,icnt,mpi_err) |
| 387 |
|
| 388 |
call mpi_recv(atom_index_tmp,3*icnt,mpi_integer,iproc,0, & |
| 389 |
mpi_comm_world,istatus,mpi_err) |
| 390 |
if (mpi_err /= 0) then |
| 391 |
call error("DUMP_CONFIG","Error recieving atom_index") |
| 392 |
endif |
| 393 |
|
| 394 |
call mpi_recv(ident_tmp,max_local,mpi_integer,iproc,0, & |
| 395 |
mpi_comm_world,istatus,mpi_err) |
| 396 |
if (mpi_err /= 0) then |
| 397 |
call error("DUMP_CONFIG","Error recieving ident_tmp") |
| 398 |
endif |
| 399 |
|
| 400 |
call mpi_get_count(istatus,mpi_integer,i_a_cnt,mpi_err) |
| 401 |
|
| 402 |
call mpi_recv(q_tmp,3*i_a_cnt,mpi_double_precision,iproc,0, & |
| 403 |
mpi_comm_world,istatus,mpi_err) |
| 404 |
if (mpi_err /= 0) then |
| 405 |
call error("DUMP_CONFIG","Error recieving q_tmp") |
| 406 |
endif |
| 407 |
|
| 408 |
call mpi_recv(v_tmp,3*i_a_cnt,mpi_double_precision,iproc,0, & |
| 409 |
mpi_comm_world,istatus,mpi_err) |
| 410 |
if (mpi_err /= 0) then |
| 411 |
call error("DUMP_CONFIG","Error recieving v_tmp") |
| 412 |
endif |
| 413 |
|
| 414 |
|
| 415 |
do i = 1,icnt |
| 416 |
do a = 1, na_tmp(i) |
| 417 |
atom = atom_index_tmp(i,a) |
| 418 |
atid = atype_identifier(ident_tmp(atom)) // ' ' |
| 419 |
write(dump_unit,fmt=xyz_coord) atid, q_tmp(1,atom), & |
| 420 |
q_tmp(2,atom), q_tmp(3,atom), v_tmp(1,atom), & |
| 421 |
v_tmp(2,atom), v_tmp(3,atom), ident_tmp(atom) |
| 422 |
end do |
| 423 |
enddo |
| 424 |
|
| 425 |
end do |
| 426 |
endif |
| 427 |
|
| 428 |
call mpi_barrier(mpi_comm_world,mpi_err) |
| 429 |
|
| 430 |
if (node == 0) & |
| 431 |
call machdep_flush(dump_unit) |
| 432 |
#endif |
| 433 |
end subroutine dump_config |
| 434 |
|
| 435 |
|
| 436 |
subroutine write_final_config() |
| 437 |
! Reads In the current configuration in XYZ file format. The next |
| 438 |
! frame in XYZ is simply appended to the end of the current frame. |
| 439 |
|
| 440 |
include 'headers/atom.h' |
| 441 |
|
| 442 |
character(len = 80) :: eor_file |
| 443 |
character(len = 120) :: msg |
| 444 |
integer err |
| 445 |
|
| 446 |
#ifdef MPI |
| 447 |
integer, dimension(maxmol_local) :: na_tmp |
| 448 |
integer, dimension(maxmol_local,3) :: atom_index_tmp |
| 449 |
integer, dimension(max_local) :: ident_tmp |
| 450 |
#endif |
| 451 |
integer ::i,j, iproc, a |
| 452 |
integer :: atom |
| 453 |
integer :: icnt, i_a_cnt |
| 454 |
|
| 455 |
character(len=10) :: chartmp |
| 456 |
|
| 457 |
|
| 458 |
|
| 459 |
|
| 460 |
#ifdef MPI |
| 461 |
if (node == 0) then |
| 462 |
#endif |
| 463 |
eor_unit = next_unit() |
| 464 |
|
| 465 |
eor_file = file_prefix(1:machdep_lnblnk(file_prefix)) // '.eor' |
| 466 |
open(file=eor_file, unit=eor_unit, status='replace', iostat= err, & |
| 467 |
action='write') |
| 468 |
|
| 469 |
if (err > 0) then |
| 470 |
write(msg,*) "Error opening eor file", trim(eor_file) |
| 471 |
call info("DUMP_FINAL_CONFIG", msg) |
| 472 |
end if |
| 473 |
write(msg,*) 'final configuration will be in: ', trim(eor_file) |
| 474 |
call info("DUMP_FINAL_CONFIG", msg) |
| 475 |
|
| 476 |
#ifdef MPI |
| 477 |
endif |
| 478 |
#endif |
| 479 |
|
| 480 |
|
| 481 |
|
| 482 |
|
| 483 |
|
| 484 |
|
| 485 |
|
| 486 |
|
| 487 |
#ifndef MPI |
| 488 |
|
| 489 |
|
| 490 |
write(eor_unit,fmt=xyz_line1) natoms |
| 491 |
write(eor_unit,*) |
| 492 |
|
| 493 |
do i = 1, natoms |
| 494 |
do a = 1, na(i) |
| 495 |
atom = atom_index(i,a) |
| 496 |
atid = atype_identifier(ident(atom)) // ' ' |
| 497 |
write(eor_unit,fmt=xyz_coord) atid, q(1,atom), q(2,atom), q(3,atom), & |
| 498 |
v(1,atom), v(2,atom), v(3,atom), ident(i) |
| 499 |
end do |
| 500 |
end do |
| 501 |
|
| 502 |
close(eor_unit) |
| 503 |
#else |
| 504 |
|
| 505 |
if (node /= 0) then |
| 506 |
|
| 507 |
call mpi_send(na,nmol_local,mpi_integer,0,0, & |
| 508 |
mpi_comm_world,mpi_err) |
| 509 |
if (mpi_err /= 0) then |
| 510 |
call error("WRITE_FINALCONFIG","Error sending na") |
| 511 |
endif |
| 512 |
call mpi_send(atom_index,3*nmol_local,mpi_integer,0,0, & |
| 513 |
mpi_comm_world,mpi_err) |
| 514 |
if (mpi_err /= 0) then |
| 515 |
call error("WRITE_FINALCONFIG","Error sending atom_index") |
| 516 |
endif |
| 517 |
call mpi_send(ident,nlocal,mpi_integer,0,0, & |
| 518 |
mpi_comm_world,mpi_err) |
| 519 |
if (mpi_err /= 0) then |
| 520 |
call error("WRITE_FINALCONFIG","Error sending ident") |
| 521 |
endif |
| 522 |
call mpi_send(q,3*nlocal,mpi_double_precision,0,0, & |
| 523 |
mpi_comm_world,mpi_err) |
| 524 |
if (mpi_err /= 0) then |
| 525 |
call error("WRITE_FINALCONFIG","Error sending q") |
| 526 |
endif |
| 527 |
call mpi_send(v,3*nlocal,mpi_double_precision,0,0, & |
| 528 |
mpi_comm_world,mpi_err) |
| 529 |
if (mpi_err /= 0) then |
| 530 |
call error("WRITE_FINALCONFIG","Error sending v") |
| 531 |
endif |
| 532 |
|
| 533 |
else |
| 534 |
|
| 535 |
|
| 536 |
write(eor_unit,*) natoms |
| 537 |
write(eor_unit,*) |
| 538 |
|
| 539 |
|
| 540 |
do i = 1, nlocal |
| 541 |
charident = atype_identifier(ident(i)) // ' ' |
| 542 |
write(unit=eor_unit,fmt=xyz_coord) charident, (q(j,i),j=1,3), & |
| 543 |
(v(j,i),j=1,3), ident(i) |
| 544 |
end do |
| 545 |
|
| 546 |
do iproc = 1,nprocs - 1 |
| 547 |
icnt = 0 |
| 548 |
|
| 549 |
call mpi_recv(na_tmp, maxmol_local, mpi_integer,iproc,0, & |
| 550 |
mpi_comm_world,istatus,mpi_err) |
| 551 |
if (mpi_err /= 0) then |
| 552 |
call error("WRITE_FINALCONFIG","Error receiving na_tmp") |
| 553 |
endif |
| 554 |
|
| 555 |
call mpi_get_count(istatus,mpi_integer,icnt,mpi_err) |
| 556 |
|
| 557 |
call mpi_recv(atom_index_tmp,3*icnt,mpi_integer,iproc,0, & |
| 558 |
mpi_comm_world,istatus,mpi_err) |
| 559 |
if (mpi_err /= 0) then |
| 560 |
call error("WRITE_FINALCONFIG","Error receiving atom_index_tmp") |
| 561 |
endif |
| 562 |
|
| 563 |
call mpi_recv(ident_tmp,max_local,mpi_integer,iproc,0, & |
| 564 |
mpi_comm_world,istatus,mpi_err) |
| 565 |
if (mpi_err /= 0) then |
| 566 |
call error("WRITE_FINAL_CONFIG","Error receiving ident_tmp") |
| 567 |
endif |
| 568 |
|
| 569 |
call mpi_get_count(istatus,mpi_integer,i_a_cnt,mpi_err) |
| 570 |
call mpi_recv(q_tmp,3*i_a_cnt,mpi_double_precision,iproc,0, & |
| 571 |
mpi_comm_world,istatus,mpi_err) |
| 572 |
if (mpi_err /= 0) then |
| 573 |
call error("WRITE_FINAL_CONFIG","Error receiving q_tmp") |
| 574 |
endif |
| 575 |
call mpi_recv(v_tmp,3*i_a_cnt,mpi_double_precision,iproc,0, & |
| 576 |
mpi_comm_world,istatus,mpi_err) |
| 577 |
if (mpi_err /= 0) then |
| 578 |
call error("WRITE_FINAL_CONFIG","Error receiving v_tmp") |
| 579 |
endif |
| 580 |
|
| 581 |
|
| 582 |
do i = 1,icnt |
| 583 |
do a = 1, na_tmp(i) |
| 584 |
atom = atom_index_tmp(i,a) |
| 585 |
atid = atype_identifier(ident_tmp(atom)) // ' ' |
| 586 |
write(eor_unit,fmt=xyz_coord) atid, q_tmp(1,atom), & |
| 587 |
q_tmp(2,atom), q_tmp(3,atom), v_tmp(1,atom), & |
| 588 |
v_tmp(2,atom), v_tmp(3,atom), ident_tmp(atom) |
| 589 |
end do |
| 590 |
enddo |
| 591 |
|
| 592 |
end do |
| 593 |
endif |
| 594 |
|
| 595 |
call mpi_barrier(mpi_comm_world,mpi_err) |
| 596 |
|
| 597 |
if (node == 0) then |
| 598 |
call machdep_flush(eor_unit) |
| 599 |
close(eor_unit) |
| 600 |
end if |
| 601 |
#endif |
| 602 |
end subroutine write_final_config |
| 603 |
|
| 604 |
|
| 605 |
subroutine dump_forces(this_time) |
| 606 |
! Reads In the current configuration in XYZ file format. The next |
| 607 |
! frame in XYZ is simply appended to the end of the current frame. |
| 608 |
|
| 609 |
! include 'headers/fileio.h' |
| 610 |
! include 'headers/atom.h' |
| 611 |
|
| 612 |
real( kind=DP ), intent(in) :: this_time |
| 613 |
integer ::i,j, iproc, a |
| 614 |
#ifdef MPI |
| 615 |
integer, dimension(max_local) :: tag_tmp |
| 616 |
#endif |
| 617 |
integer :: icnt |
| 618 |
character(Len=*), parameter :: forcefmt = '(I3,3es18.8)' |
| 619 |
|
| 620 |
#ifdef MPI |
| 621 |
if (node /= 0) then |
| 622 |
|
| 623 |
call mpi_send(tag_local,nlocal,mpi_integer,0,0, & |
| 624 |
mpi_comm_world,mpi_err) |
| 625 |
|
| 626 |
call mpi_send(f,3*nlocal,mpi_double_precision,0,0, & |
| 627 |
mpi_comm_world,mpi_err) |
| 628 |
|
| 629 |
call mpi_send(rho,nlocal,mpi_double_precision,0,0, & |
| 630 |
mpi_comm_world,mpi_err) |
| 631 |
|
| 632 |
! call mpi_send(frho,nlocal,mpi_double_precision,0,0, & |
| 633 |
! mpi_comm_world,mpi_err) |
| 634 |
|
| 635 |
else |
| 636 |
|
| 637 |
write(force_unit,'(es12.4)') this_time |
| 638 |
|
| 639 |
|
| 640 |
do i = 1, nlocal |
| 641 |
write(unit=force_unit,fmt=*) tag_local(i),rho(i),f(1,i), & |
| 642 |
f(2,i),f(3,i) |
| 643 |
end do |
| 644 |
|
| 645 |
do iproc = 1,nprocs - 1 |
| 646 |
icnt = 0 |
| 647 |
f_tmp = 0.0d0 |
| 648 |
|
| 649 |
|
| 650 |
call mpi_recv(tag_tmp,max_local,mpi_integer,iproc,0, & |
| 651 |
mpi_comm_world,istatus,mpi_err) |
| 652 |
call mpi_get_count(istatus,mpi_integer,icnt,mpi_err) |
| 653 |
call mpi_recv(f_tmp,3*icnt,mpi_double_precision,iproc,0, & |
| 654 |
mpi_comm_world,istatus,mpi_err) |
| 655 |
call mpi_recv(rho_tmp,icnt,mpi_double_precision,iproc,0, & |
| 656 |
mpi_comm_world,istatus,mpi_err) |
| 657 |
! call mpi_recv(frho_tmp,icnt,mpi_double_precision,iproc,0, & |
| 658 |
! mpi_comm_world,istatus,mpi_err) |
| 659 |
|
| 660 |
|
| 661 |
do i = 1,icnt |
| 662 |
write(unit=force_unit,fmt=*) tag_tmp(i),rho_tmp(i), & |
| 663 |
f_tmp(1,i),f_tmp(2,i),f_tmp(3,i) |
| 664 |
enddo |
| 665 |
|
| 666 |
end do |
| 667 |
endif |
| 668 |
|
| 669 |
call mpi_barrier(mpi_comm_world,mpi_err) |
| 670 |
|
| 671 |
if (node == 0) then |
| 672 |
call machdep_flush(dump_unit) |
| 673 |
end if |
| 674 |
#else |
| 675 |
write(force_unit,'(es12.4)') this_time |
| 676 |
do i = 1, natoms |
| 677 |
write(unit=force_unit,fmt=*) i,rho(i),f(1,i), & |
| 678 |
f(2,i),f(3,i) |
| 679 |
end do |
| 680 |
|
| 681 |
#endif |
| 682 |
|
| 683 |
end subroutine dump_forces |
| 684 |
|
| 685 |
|
| 686 |
!! remove me |
| 687 |
#ifdef MPI |
| 688 |
subroutine mpi_dump_q() |
| 689 |
integer, parameter :: q_row_unit = 110 |
| 690 |
integer, parameter :: q_col_unit = 111 |
| 691 |
integer :: processor |
| 692 |
integer :: i, err |
| 693 |
integer :: nrow_count,ncol_count |
| 694 |
character(len=60) :: q_row_file,q_col_file,q_file |
| 695 |
character(len=5) :: char_node |
| 696 |
real(kind=8), dimension(3,max_row) :: q_row_tmp |
| 697 |
real(kind=8), dimension(3,max_col) :: q_col_tmp |
| 698 |
integer, dimension(max_row) :: tag_row_tmp,ident_row_tmp |
| 699 |
integer, dimension(max_col) :: tag_col_tmp,ident_col_tmp |
| 700 |
integer :: nrow_tmp, ncol_tmp, nlocal_tmp |
| 701 |
|
| 702 |
if (node /= 0 ) then |
| 703 |
call mpi_send(nlocal,1,mpi_integer,0,0,mpi_comm_world,mpi_err) |
| 704 |
call mpi_send(nrow,1,mpi_integer,0,0,mpi_comm_world,mpi_err) |
| 705 |
call mpi_send(ncol,1,mpi_integer,0,0,mpi_comm_world,mpi_err) |
| 706 |
call mpi_send(ident_row,nrow,mpi_integer,0,0, & |
| 707 |
mpi_comm_world,mpi_err) |
| 708 |
call mpi_send(ident_col,ncol,mpi_integer,0,0, & |
| 709 |
mpi_comm_world,mpi_err) |
| 710 |
call mpi_send(q_row,3*nrow,mpi_double_precision,0,0, & |
| 711 |
mpi_comm_world,mpi_err) |
| 712 |
call mpi_send(q_col,3*ncol,mpi_double_precision,0,0, & |
| 713 |
mpi_comm_world,mpi_err) |
| 714 |
call mpi_send(tag_row,nrow,mpi_integer,0,0, & |
| 715 |
mpi_comm_world,mpi_err) |
| 716 |
call mpi_send(tag_col,ncol,mpi_integer,0,0, & |
| 717 |
mpi_comm_world,mpi_err) |
| 718 |
else |
| 719 |
|
| 720 |
!! node 0 writes its arrays first |
| 721 |
write(char_node,"(a1,i1,a1)") "_",node,"_" |
| 722 |
char_node = trim(char_node) |
| 723 |
q_row_file = file_prefix(1:machdep_lnblnk(file_prefix)) // & |
| 724 |
char_node(1:machdep_lnblnk(char_node)) // & |
| 725 |
'.row' |
| 726 |
open(file=q_row_file, unit=q_row_unit, status='replace', iostat= err, & |
| 727 |
action='write') |
| 728 |
write(unit=q_row_unit,fmt="(i5,i5)") node,nrow |
| 729 |
do i = 1, nrow |
| 730 |
write(unit=q_row_unit,fmt="(i5,3es12.4,i4)") tag_row(i),q_row(1,i), & |
| 731 |
q_row(2,i), q_row(3,i), ident_row(i) |
| 732 |
end do |
| 733 |
|
| 734 |
close(unit=q_row_unit) |
| 735 |
|
| 736 |
q_col_file = file_prefix(1:machdep_lnblnk(file_prefix)) // & |
| 737 |
char_node(1:machdep_lnblnk(char_node)) // & |
| 738 |
'.col' |
| 739 |
open(file=q_col_file, unit=q_col_unit, status='replace', iostat= err, & |
| 740 |
action='write') |
| 741 |
write(unit=q_col_unit,fmt="(i5,i5)") node,ncol |
| 742 |
do i = 1, ncol |
| 743 |
write(unit=q_col_unit,fmt="(i5,3es12.4,i4)") tag_col(i),q_col(1,i), q_col(2,i), & |
| 744 |
q_col(3,i), ident_col(i) |
| 745 |
end do |
| 746 |
|
| 747 |
close(unit=q_col_unit) |
| 748 |
write(*,*) node, nlocal, nrow, ncol |
| 749 |
do processor = 1, nprocs - 1 |
| 750 |
!! recv data from other procs |
| 751 |
call mpi_recv(nlocal_tmp,1,mpi_integer,processor,0,mpi_comm_world,& |
| 752 |
istatus,mpi_err) |
| 753 |
call mpi_recv(nrow_tmp,1,mpi_integer,processor,0,mpi_comm_world,& |
| 754 |
istatus,mpi_err) |
| 755 |
call mpi_recv(ncol_tmp,1,mpi_integer,processor,0,mpi_comm_world,& |
| 756 |
istatus,mpi_err) |
| 757 |
write(*,*) processor, nlocal_tmp, nrow_tmp, ncol_tmp |
| 758 |
call mpi_recv(ident_row_tmp,nrow_tmp,mpi_integer,processor,0, & |
| 759 |
mpi_comm_world,istatus,mpi_err) |
| 760 |
write(*,*) "Past ident row" |
| 761 |
! call mpi_get_count(istatus,mpi_integer, nrow_count,mpi_err) |
| 762 |
call mpi_recv(ident_col_tmp,ncol_tmp,mpi_integer,processor,0, & |
| 763 |
mpi_comm_world,istatus,mpi_err) |
| 764 |
! call mpi_get_count(istatus,mpi_integer,ncol_count,mpi_err) |
| 765 |
write(*,*) "Past ident_col " |
| 766 |
call mpi_recv(q_row_tmp,3*nrow_tmp,mpi_double_precision,processor,0,& |
| 767 |
mpi_comm_world,istatus,mpi_err) |
| 768 |
write(*,*) "Past q_row" |
| 769 |
call mpi_recv(q_col_tmp,3*ncol_tmp,mpi_double_precision,processor,0,& |
| 770 |
mpi_comm_world,istatus,mpi_err) |
| 771 |
write(*,*) "Past q_col" |
| 772 |
call mpi_recv(tag_row_tmp,nrow_tmp,mpi_integer,processor,0, & |
| 773 |
mpi_comm_world,istatus,mpi_err) |
| 774 |
write(*,*) "Past tag row" |
| 775 |
call mpi_recv(tag_col_tmp,ncol_tmp,mpi_integer,processor,0, & |
| 776 |
mpi_comm_world,istatus,mpi_err) |
| 777 |
write(*,*) "Past tag col" |
| 778 |
write(char_node,"(a1,i1,a1)") "_",processor,"_" |
| 779 |
char_node = trim(char_node) |
| 780 |
q_row_file = file_prefix(1:machdep_lnblnk(file_prefix)) // & |
| 781 |
char_node(1:machdep_lnblnk(char_node)) // '.row' |
| 782 |
open(file=q_row_file, unit=q_row_unit, status='replace', iostat= err, & |
| 783 |
action='write') |
| 784 |
write(unit=q_row_unit,fmt="(i5,i5)") node,nrow |
| 785 |
do i = 1, nrow_tmp |
| 786 |
write(unit=q_row_unit,fmt="(i5,3es12.4,i4)") tag_row_tmp(i),q_row_tmp(1,i), & |
| 787 |
q_row_tmp(2,i),q_row_tmp(3,i), ident_row_tmp(i) |
| 788 |
end do |
| 789 |
|
| 790 |
close(unit=q_row_unit) |
| 791 |
|
| 792 |
q_col_file = file_prefix(1:machdep_lnblnk(file_prefix)) // & |
| 793 |
char_node(1:machdep_lnblnk(char_node)) // & |
| 794 |
'.col' |
| 795 |
open(file=q_col_file, unit=q_col_unit, status='replace', iostat= err, & |
| 796 |
action='write') |
| 797 |
write(unit=q_col_unit,fmt="(i5,i5)") node,ncol |
| 798 |
do i = 1, ncol_tmp |
| 799 |
write(unit=q_col_unit,fmt="(i5,3es12.4,i4)") tag_col_tmp(i),q_col_tmp(1,i), & |
| 800 |
q_col_tmp(2,i), q_col_tmp(3,i), ident_col_tmp(i) |
| 801 |
end do |
| 802 |
|
| 803 |
close(unit=q_col_unit) |
| 804 |
enddo |
| 805 |
|
| 806 |
endif |
| 807 |
call mpi_barrier(mpi_comm_world,mpi_err) |
| 808 |
end subroutine mpi_dump_q |
| 809 |
|
| 810 |
#endif |
| 811 |
|
| 812 |
end module xyz_io |
