106 CHARACTER(len=*),
PARAMETER :: routinen =
'read_coordinate_pdb'
107 INTEGER,
PARAMETER :: nblock = 1000
109 CHARACTER(LEN=default_path_length) :: line
110 CHARACTER(LEN=default_string_length) :: record, root_mol_name, strtmp
111 INTEGER :: handle, id0, inum_mol, istat, iw, natom, &
114 REAL(kind=
dp) :: pfactor
122 extension=
".subsysLog")
123 CALL timeset(routinen, handle)
125 pfactor =
section_get_rval(subsys_section,
"TOPOLOGY%MEMORY_PROGRESSION_FACTOR")
127 CALL reallocate(atom_info%id_molname, 1, nblock)
128 CALL reallocate(atom_info%id_resname, 1, nblock)
130 CALL reallocate(atom_info%id_atmname, 1, nblock)
132 CALL reallocate(atom_info%atm_mass, 1, nblock)
133 CALL reallocate(atom_info%atm_charge, 1, nblock)
136 CALL reallocate(atom_info%id_element, 1, nblock)
139 WRITE (unit=iw, fmt=
"(T2,A)") &
140 "BEGIN of PDB data read from file "//trim(
topology%coord_file_name)
144 topology%molname_generated = .false.
150 WRITE (unit=root_mol_name, fmt=
'(A3,I0)')
"MOL", inum_mol
157 record = trim(record)
159 IF ((record ==
"ATOM") .OR. (record ==
"HETATM"))
THEN
162 IF (natom >
SIZE(atom_info%id_atmname))
THEN
163 newsize = int(pfactor*natom)
164 CALL reallocate(atom_info%id_molname, 1, newsize)
165 CALL reallocate(atom_info%id_resname, 1, newsize)
167 CALL reallocate(atom_info%id_atmname, 1, newsize)
168 CALL reallocate(atom_info%r, 1, 3, 1, newsize)
169 CALL reallocate(atom_info%atm_mass, 1, newsize)
170 CALL reallocate(atom_info%atm_charge, 1, newsize)
173 CALL reallocate(atom_info%id_element, 1, newsize)
178 CASE (
"ATOM",
"HETATM")
179 READ (unit=line(13:16), fmt=*) strtmp
180 atom_info%id_atmname(natom) =
str2id(
s2s(strtmp))
181 READ (unit=line(18:20), fmt=*, iostat=istat) strtmp
183 atom_info%id_resname(natom) =
str2id(
s2s(strtmp))
185 atom_info%id_resname(natom) = id0
187 READ (unit=line(23:26), fmt=*, iostat=istat) atom_info%resid(natom)
188 READ (unit=line(31:38), fmt=*, iostat=istat) atom_info%r(1, natom)
189 READ (unit=line(39:46), fmt=*, iostat=istat) atom_info%r(2, natom)
190 READ (unit=line(47:54), fmt=*, iostat=istat) atom_info%r(3, natom)
191 READ (unit=line(55:60), fmt=*, iostat=istat) atom_info%occup(natom)
192 READ (unit=line(61:66), fmt=*, iostat=istat) atom_info%beta(natom)
193 READ (unit=line(73:76), fmt=*, iostat=istat) strtmp
195 atom_info%id_molname(natom) =
str2id(
s2s(strtmp))
197 atom_info%id_molname(natom) =
str2id(
s2s(root_mol_name))
200 READ (unit=line(77:78), fmt=*, iostat=istat) strtmp
202 atom_info%id_element(natom) =
str2id(
s2s(strtmp))
204 atom_info%id_element(natom) = id0
206 atom_info%atm_mass(natom) = 0.0_dp
207 atom_info%atm_charge(natom) = -huge(0.0_dp)
208 IF (
topology%charge_occup) atom_info%atm_charge(natom) = atom_info%occup(natom)
209 IF (
topology%charge_beta) atom_info%atm_charge(natom) = atom_info%beta(natom)
211 READ (unit=line(81:), fmt=*, iostat=istat) atom_info%atm_charge(natom)
214 IF (atom_info%id_element(natom) == id0)
THEN
217 atom_info%id_element(natom) = atom_info%id_atmname(natom)
221 WRITE (unit=iw, fmt=
"(A6,I5,T13,A4,T18,A3,T23,I4,T31,3F8.3,T73,A4,T77,A2)") &
223 trim(
id2str(atom_info%id_atmname(natom))), &
224 trim(
id2str(atom_info%id_resname(natom))), &
225 atom_info%resid(natom), &
226 atom_info%r(1, natom), &
227 atom_info%r(2, natom), &
228 atom_info%r(3, natom), &
229 adjustl(trim(
id2str(atom_info%id_molname(natom)))), &
230 adjustr(trim(
id2str(atom_info%id_element(natom))))
232 atom_info%r(1, natom) =
cp_unit_to_cp2k(atom_info%r(1, natom),
"angstrom")
233 atom_info%r(2, natom) =
cp_unit_to_cp2k(atom_info%r(2, natom),
"angstrom")
234 atom_info%r(3, natom) =
cp_unit_to_cp2k(atom_info%r(3, natom),
"angstrom")
236 inum_mol = inum_mol + 1
237 WRITE (unit=root_mol_name, fmt=
'(A3,I0)')
"MOL", inum_mol
239 IF (iw > 0)
WRITE (unit=iw, fmt=*) trim(line)
247 CALL reallocate(atom_info%id_molname, 1, natom)
248 CALL reallocate(atom_info%id_resname, 1, natom)
250 CALL reallocate(atom_info%id_atmname, 1, natom)
253 CALL reallocate(atom_info%atm_charge, 1, natom)
256 CALL reallocate(atom_info%id_element, 1, natom)
259 IF (.NOT.
topology%para_res) atom_info%resid(:) = 1
263 WRITE (unit=iw, fmt=
"(T2,A)") &
264 "END of PDB data read from file "//trim(
topology%coord_file_name)
269 "PRINT%TOPOLOGY_INFO/PDB_INFO")
270 CALL timestop(handle)
282 INTEGER,
INTENT(IN) :: file_unit
286 CHARACTER(len=*),
PARAMETER :: routinen =
'write_coordinate_pdb'
288 CHARACTER(LEN=120) :: line
289 CHARACTER(LEN=default_string_length) :: my_tag1, my_tag2, my_tag3, my_tag4, &
291 INTEGER :: handle, i, id1, id2, idres, iw, natom
292 LOGICAL :: charge_beta, charge_extended, &
294 REAL(kind=
dp) :: angle_alpha, angle_beta, angle_gamma
295 REAL(kind=
dp),
DIMENSION(3) :: abc
303 extension=
".subsysLog")
305 CALL timeset(routinen, handle)
310 i = count((/charge_occup, charge_beta, charge_extended/))
312 cpabort(
"Either only CHARGE_OCCUP, CHARGE_BETA, or CHARGE_EXTENDED can be selected")
319 IF (iw > 0)
WRITE (unit=iw, fmt=*)
" Writing out PDB file ", trim(record)
322 WRITE (unit=file_unit, fmt=
"(A6,T11,A)") &
327 WRITE (unit=file_unit, fmt=
"(A6,3F9.3,3F7.2)") &
328 "CRYST1", abc(1:3)*
angstrom, angle_alpha, angle_beta, angle_gamma
338 idres = atom_info%resid(i)
340 IF ((id1 /= atom_info%map_mol_num(i)) .OR. (id2 /= atom_info%map_mol_typ(i)))
THEN
342 id1 = atom_info%map_mol_num(i)
343 id2 = atom_info%map_mol_typ(i)
353 WRITE (unit=line(1:6), fmt=
"(A6)")
"ATOM "
354 WRITE (unit=line(7:11), fmt=
"(I5)")
modulo(i, 100000)
355 WRITE (unit=line(13:16), fmt=
"(A4)") adjustl(my_tag1(1:4))
356 WRITE (unit=line(18:20), fmt=
"(A3)") trim(my_tag2)
357 WRITE (unit=line(23:26), fmt=
"(I4)")
modulo(idres, 10000)
358 WRITE (unit=line(31:54), fmt=
"(3F8.3)") atom_info%r(1:3, i)*
angstrom
359 IF (
ASSOCIATED(atom_info%occup))
THEN
360 WRITE (unit=line(55:60), fmt=
"(F6.2)") atom_info%occup(i)
362 WRITE (unit=line(55:60), fmt=
"(F6.2)") 0.0_dp
364 IF (
ASSOCIATED(atom_info%beta))
THEN
365 WRITE (unit=line(61:66), fmt=
"(F6.2)") atom_info%beta(i)
367 WRITE (unit=line(61:66), fmt=
"(F6.2)") 0.0_dp
369 IF (
ASSOCIATED(atom_info%atm_charge))
THEN
370 IF (any((/charge_occup, charge_beta, charge_extended/)) .AND. &
371 (atom_info%atm_charge(i) == -huge(0.0_dp))) &
372 cpabort(
"No atomic charges found yet (after the topology setup)")
373 IF (charge_occup)
THEN
374 WRITE (unit=line(55:60), fmt=
"(F6.2)") atom_info%atm_charge(i)
375 ELSE IF (charge_beta)
THEN
376 WRITE (unit=line(61:66), fmt=
"(F6.2)") atom_info%atm_charge(i)
377 ELSE IF (charge_extended)
THEN
378 WRITE (unit=line(81:), fmt=
"(F20.16)") atom_info%atm_charge(i)
383 WRITE (unit=line(73:76), fmt=
"(A4)") adjustl(my_tag3)
384 WRITE (unit=line(77:78), fmt=
"(A2)") trim(my_tag4)
385 WRITE (unit=file_unit, fmt=
"(A)") trim(line)
387 WRITE (unit=file_unit, fmt=
"(A3)")
"END"
389 IF (iw > 0)
WRITE (unit=iw, fmt=*)
" Exiting "//routinen
392 "PRINT%TOPOLOGY_INFO/PDB_INFO")
394 CALL timestop(handle)