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
|
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "compute_inertia_molecule.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeInertiaMolecule::
ComputeInertiaMolecule(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute inertia/molecule command");
if (atom->molecular == 0)
error->all(FLERR,"Compute inertia/molecule requires molecular atom style");
array_flag = 1;
size_array_cols = 6;
extarray = 0;
// setup molecule-based data
nmolecules = molecules_in_group(idlo,idhi);
size_array_rows = nmolecules;
memory->create(massproc,nmolecules,"inertia/molecule:massproc");
memory->create(masstotal,nmolecules,"inertia/molecule:masstotal");
memory->create(com,nmolecules,3,"inertia/molecule:com");
memory->create(comall,nmolecules,3,"inertia/molecule:comall");
memory->create(inertia,nmolecules,6,"inertia/molecule:inertia");
memory->create(inertiaall,nmolecules,6,"inertia/molecule:inertiaall");
array = inertiaall;
// compute masstotal for each molecule
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
tagint imol;
double massone;
for (int i = 0; i < nmolecules; i++) massproc[i] = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
imol = molecule[i];
if (molmap) imol = molmap[imol-idlo];
else imol--;
massproc[imol] += massone;
}
MPI_Allreduce(massproc,masstotal,nmolecules,MPI_DOUBLE,MPI_SUM,world);
}
/* ---------------------------------------------------------------------- */
ComputeInertiaMolecule::~ComputeInertiaMolecule()
{
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(inertia);
memory->destroy(inertiaall);
}
/* ---------------------------------------------------------------------- */
void ComputeInertiaMolecule::init()
{
int ntmp = molecules_in_group(idlo,idhi);
if (ntmp != nmolecules)
error->all(FLERR,"Molecule count changed in compute inertia/molecule");
}
/* ---------------------------------------------------------------------- */
void ComputeInertiaMolecule::compute_array()
{
int i,j;
tagint imol;
double dx,dy,dz,massone;
double unwrap[3];
invoked_array = update->ntimestep;
double **x = atom->x;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
// center-of-mass for each molecule
for (i = 0; i < nmolecules; i++)
com[i][0] = com[i][1] = com[i][2] = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
imol = molecule[i];
if (molmap) imol = molmap[imol-idlo];
else imol--;
domain->unmap(x[i],image[i],unwrap);
com[imol][0] += unwrap[0] * massone;
com[imol][1] += unwrap[1] * massone;
com[imol][2] += unwrap[2] * massone;
}
MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < nmolecules; i++) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[i][2] /= masstotal[i];
}
// inertia tensor for each molecule
for (i = 0; i < nmolecules; i++)
for (j = 0; j < 6; j++)
inertia[i][j] = 0.0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
imol = molecule[i];
if (molmap) imol = molmap[imol-idlo];
else imol--;
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - comall[imol][0];
dy = unwrap[1] - comall[imol][1];
dz = unwrap[2] - comall[imol][2];
inertia[imol][0] += massone * (dy*dy + dz*dz);
inertia[imol][1] += massone * (dx*dx + dz*dz);
inertia[imol][2] += massone * (dx*dx + dy*dy);
inertia[imol][3] -= massone * dx*dy;
inertia[imol][4] -= massone * dy*dz;
inertia[imol][5] -= massone * dx*dz;
}
MPI_Allreduce(&inertia[0][0],&inertiaall[0][0],6*nmolecules,
MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeInertiaMolecule::memory_usage()
{
double bytes = (bigint) nmolecules * 2 * sizeof(double);
if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
bytes += (bigint) nmolecules * 2*3 * sizeof(double);
bytes += (bigint) nmolecules * 2*6 * sizeof(double);
return bytes;
}
|
