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
|
!
! Copyright (C) 2013 Quantum ESPRESSO groups
! This file is distributed under the terms of the
! GNU General Public License. See the file `License'
! in the root directory of the present distribution,
! or http://www.gnu.org/copyleft/gpl.txt .
!
!==-----------------------------------------------------------------------==!
MODULE qmmm
!==---------------------------------------------------------------------==!
USE io_global, ONLY : ionode, ionode_id, stdout
USE mp_world, ONLY : world_comm
USE mp, ONLY : mp_bcast, mp_barrier, mp_abort
USE kinds, ONLY : DP
USE parallel_include
IMPLICIT NONE
!
SAVE
!
PRIVATE
!
! ... MPI communicator to the QM/MM control process, if MPI is used
INTEGER :: qmmm_comm = MPI_COMM_NULL
! ... number of QM/MM steps
INTEGER :: qmmm_step = -1
!
INTEGER :: qmmm_mode = -1
! mode = <0: QM/MM disabled
! mode = 0: not properly set up
! mode = 1: mechanical coupling
! mode = 2: electrostatic coupling
!
! verbosity level
INTEGER :: qmmm_verb = -1
!
! message tags. keep consistent with MM code
INTEGER, PARAMETER :: QMMM_TAG_OTHER=0
INTEGER, PARAMETER :: QMMM_TAG_SIZE=1
INTEGER, PARAMETER :: QMMM_TAG_COORD=2
INTEGER, PARAMETER :: QMMM_TAG_FORCE=3
!
! convert forces to LAMMPS "real" units
REAL(DP), PARAMETER :: QMMM_FORCE_CONV = 592.91102087727177_DP
!
! Number of atoms of the QM/MM systems
INTEGER :: nat_qm
! buffer for converting forces and positions
REAL(DP), ALLOCATABLE :: tmp_buf(:,:)
! center of mass of the system
REAL(DP), DIMENSION(3) :: r0 = (/ 0.0_DP, 0.0_DP, 0.0_DP /)
LOGICAL :: do_init_r0 = .TRUE.
PUBLIC :: qmmm_config, qmmm_initialization, qmmm_shutdown
PUBLIC :: qmmm_update_positions, qmmm_update_forces, qmmm_add_mm_field
CONTAINS
! configure the qm/mm interface
SUBROUTINE qmmm_config( mode, comm, verbose, step )
IMPLICIT NONE
INTEGER, OPTIONAL, INTENT(IN) :: mode, comm, verbose, step
IF (PRESENT(mode)) qmmm_mode = mode
IF (PRESENT(comm)) qmmm_comm = comm
IF (PRESENT(verbose)) qmmm_verb = verbose
IF (PRESENT(step)) qmmm_step = step
END SUBROUTINE qmmm_config
SUBROUTINE qmmm_initialization
USE input_parameters, ONLY : calculation, nstep, nat
!
IMPLICIT NONE
INTEGER :: ierr
IF (qmmm_mode < 0) RETURN
! send global configuration parameters to all ranks
CALL mp_bcast(qmmm_mode, ionode_id, world_comm)
CALL mp_bcast(qmmm_step, ionode_id, world_comm)
nat_qm = nat
IF (ionode) THEN
WRITE(stdout,'(/,5X,A)') "QMMM: Initializing QM/MM interface"
IF (qmmm_comm /= MPI_COMM_NULL) THEN
WRITE(stdout,'(5X,A)') "QMMM: Using MPI based communication"
ELSE
WRITE(stdout,'(5X,A)') "QMMM: Using MS2 daemon based communication"
END IF
IF (qmmm_mode == 0) THEN
WRITE(stdout,'(5X,A)') "QMMM: Running in dummy mode"
ELSE IF (qmmm_mode == 1) THEN
WRITE(stdout,'(5X,A)') "QMMM: Using mechanical coupling"
ELSE IF (qmmm_mode == 2) THEN
WRITE(stdout,'(5X,A)') "QMMM: Using electrostatic coupling"
END IF
END IF
! make sure we have sane settings
IF (TRIM( calculation ) /= 'md' ) THEN
if (ionode) &
WRITE(stdout,'(5X,A)') "QMMM Error: 'md' calculation required."
CALL mp_abort(255,world_comm)
END IF
IF (nstep /= qmmm_step) THEN
IF (ionode) WRITE(stdout,'(5X,A,I6,A,I6)') &
'QMMM: Adjusting number of steps from', nstep, ' to', qmmm_step
nstep = qmmm_step
END IF
! only ionode communicates with MM master
IF (ionode) THEN
IF (qmmm_comm /= MPI_COMM_NULL) THEN
#if defined(__MPI)
CALL mpi_send(nat_qm,1,MPI_INTEGER,0,QMMM_TAG_SIZE,qmmm_comm,ierr)
#else
WRITE(stdout,*) 'Use of QM/MM requires compilation with MPI'
STOP 200
#endif
END IF
END IF
CALL mp_bcast(nstep, ionode_id, world_comm)
! temporary storage
ALLOCATE( tmp_buf(3,nat_qm) )
END SUBROUTINE qmmm_initialization
! private subroutine
SUBROUTINE qmmm_center_molecule
USE cell_base, ONLY : alat, at
USE ions_base, ONLY : nat
USE ions_base, ONLY : tau
IMPLICIT NONE
LOGICAL, SAVE::firstexec = .TRUE.
INTEGER:: i
! New geometric center
REAL(DP), DIMENSION(3):: gc = (/0.0d0, 0.0d0, 0.0d0/)
REAL(DP), DIMENSION(3):: qm_bc = (/0.5d0, 0.5d0, 0.5d0/)
IF (firstexec) THEN
! Take the geometric center during first call
r0 = SUM(tau, dim = 2) / nat
WRITE(stdout,'(5X,A,3F10.6)') 'QMMM: r0(old) ', r0
r0 = MATMUL(at,qm_bc)
WRITE(stdout,'(5X,A,3F10.6)') 'QMMM: r0(new) ', r0
firstexec = .FALSE.
END IF
! Recenter the system.
gc = SUM(tau, dim = 2) / nat
! delta = r0 - r1
DO i = 1, nat
tau(1,i) = tau(1,i) - gc(1) + r0(1)
tau(2,i) = tau(2,i) - gc(2) + r0(2)
tau(3,i) = tau(3,i) - gc(3) + r0(3)
END DO
END SUBROUTINE qmmm_center_molecule
! update positions of the QM system from MM-master
SUBROUTINE qmmm_update_positions
USE constants, ONLY : bohr_radius_angs
USE cell_base, ONLY : alat
USE ions_base, ONLY : tau
IMPLICIT NONE
INTEGER :: ierr
IF (qmmm_mode < 0) RETURN
IF (ionode .and. (qmmm_verb > 0)) &
WRITE(stdout,'(/,5X,A)') 'QMMM: update positions'
! Receive coordinates (from LAMMPS) and broadcast to all processors
IF (ionode) THEN
#if defined(__MPI)
CALL mpi_recv(tau(1,1),3*nat_qm,MPI_DOUBLE_PRECISION, &
0,QMMM_TAG_COORD,qmmm_comm,MPI_STATUS_IGNORE,ierr)
! convert from angstrom to alat units
tau = tau / (alat * bohr_radius_angs)
#else
WRITE(stdout,*) 'Use of QM/MM requires compilation with MPI support'
STOP 201
#endif
CALL qmmm_center_molecule
END IF
CALL mp_bcast(tau, ionode_id, world_comm)
END SUBROUTINE qmmm_update_positions
! communicate forces of the QM system to MM-master
SUBROUTINE qmmm_update_forces(force)
REAL(DP), INTENT(IN) :: force(:,:)
INTEGER :: ierr
IF (qmmm_mode < 0) RETURN
IF (ionode .and. (qmmm_verb > 0)) &
WRITE(stdout,'(/,5X,A)') 'QMMM: update forces'
IF (ionode) THEN
#if defined(__MPI)
! convert from atomic to real units
tmp_buf = force * QMMM_FORCE_CONV
CALL mpi_send(tmp_buf,3*nat_qm,MPI_DOUBLE_PRECISION, &
0,QMMM_TAG_FORCE,qmmm_comm,ierr)
#else
WRITE(stdout,*) 'Use of QM/MM requires compilation with MPI support'
STOP 201
#endif
END IF
END SUBROUTINE qmmm_update_forces
! add electrostatic field of MM system to QM system
SUBROUTINE qmmm_add_mm_field
IF (qmmm_mode /= 2) RETURN
IF (ionode .and. (qmmm_verb > 0)) &
WRITE(stdout,'(/,5X,A)') 'QMMM: add mm field'
END SUBROUTINE qmmm_add_mm_field
! cleanup of QM/MM. free resources
SUBROUTINE qmmm_shutdown
IMPLICIT NONE
!
IF (qmmm_mode < 0) RETURN
IF (ionode) THEN
WRITE(stdout,'(/,5X,A)') "QMMM: Shutting down QM/MM coupling"
END IF
deallocate( tmp_buf )
END SUBROUTINE qmmm_shutdown
END MODULE qmmm
|
