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
/* ----------------------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
* This file is part of the USER-SMD package for LAMMPS.
* Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de
* Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI,
* Eckerstrasse 4, D-79104 Freiburg i.Br, Germany.
*
* ----------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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 "fix_smd_integrate_ulsph.h"
#include <cmath>
#include <cstring>
#include <Eigen/Eigen>
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "update.h"
#include "error.h"
#include "pair.h"
using namespace Eigen;
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixSMDIntegrateUlsph::FixSMDIntegrateUlsph(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg) {
if ((atom->e_flag != 1) || (atom->vfrac_flag != 1))
error->all(FLERR, "fix smd/integrate_ulsph command requires atom_style with both energy and volume");
if (narg < 3)
error->all(FLERR, "Illegal number of arguments for fix smd/integrate_ulsph command");
adjust_radius_flag = false;
xsphFlag = false;
vlimit = -1.0;
int iarg = 3;
if (comm->me == 0) {
printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
printf("fix smd/integrate_ulsph is active for group: %s \n", arg[1]);
}
while (true) {
if (iarg >= narg) {
break;
}
if (strcmp(arg[iarg], "xsph") == 0) {
xsphFlag = true;
if (comm->me == 0) {
error->one(FLERR, "XSPH is currently not available");
printf("... will use XSPH time integration\n");
}
} else if (strcmp(arg[iarg], "adjust_radius") == 0) {
adjust_radius_flag = true;
iarg++;
if (iarg == narg) {
error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max");
}
adjust_radius_factor = force->numeric(FLERR, arg[iarg]);
iarg++;
if (iarg == narg) {
error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max");
}
min_nn = force->inumeric(FLERR, arg[iarg]);
iarg++;
if (iarg == narg) {
error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max");
}
max_nn = force->inumeric(FLERR, arg[iarg]);
if (comm->me == 0) {
printf("... will adjust smoothing length dynamically with factor %g to achieve %d to %d neighbors per particle.\n ",
adjust_radius_factor, min_nn, max_nn);
}
} else if (strcmp(arg[iarg], "limit_velocity") == 0) {
iarg++;
if (iarg == narg) {
error->all(FLERR, "expected number following limit_velocity");
}
vlimit = force->numeric(FLERR, arg[iarg]);
if (comm->me == 0) {
printf("... will limit velocities to <= %g\n", vlimit);
}
} else {
char msg[128];
snprintf(msg,128, "Illegal keyword for smd/integrate_ulsph: %s\n", arg[iarg]);
error->all(FLERR, msg);
}
iarg++;
}
if (comm->me == 0) {
printf(">>========>>========>>========>>========>>========>>========>>========>>========\n\n");
}
// set comm sizes needed by this fix
atom->add_callback(0);
time_integrate = 1;
}
/* ---------------------------------------------------------------------- */
int FixSMDIntegrateUlsph::setmask() {
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixSMDIntegrateUlsph::init() {
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
vlimitsq = vlimit * vlimit;
}
/* ----------------------------------------------------------------------
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
void FixSMDIntegrateUlsph::initial_integrate(int /*vflag*/) {
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **vest = atom->vest;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int i, itmp;
double dtfm, vsq, scale;
double vxsph_x, vxsph_y, vxsph_z;
//printf("initial_integrate at timestep %d\n", update->ntimestep);
/*
* get smoothed velocities from ULSPH pair style
*/
Vector3d *smoothVel = (Vector3d *) force->pair->extract("smd/ulsph/smoothVel_ptr", itmp);
if (xsphFlag) {
if (smoothVel == NULL) {
error->one(FLERR, "fix smd/integrate_ulsph failed to access smoothVel array");
}
}
if (igroup == atom->firstgroup)
nlocal = atom->nfirst;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
if (vlimit > 0.0) {
vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
if (vsq > vlimitsq) {
scale = sqrt(vlimitsq / vsq);
v[i][0] *= scale;
v[i][1] *= scale;
v[i][2] *= scale;
vest[i][0] = v[i][0];
vest[i][1] = v[i][1];
vest[i][2] = v[i][2];
}
}
if (xsphFlag) {
// construct XSPH velocity
vxsph_x = v[i][0] - 0.5 * smoothVel[i](0);
vxsph_y = v[i][1] - 0.5 * smoothVel[i](1);
vxsph_z = v[i][2] - 0.5 * smoothVel[i](2);
vest[i][0] = vxsph_x + dtfm * f[i][0];
vest[i][1] = vxsph_y + dtfm * f[i][1];
vest[i][2] = vxsph_z + dtfm * f[i][2];
x[i][0] += dtv * vxsph_x;
x[i][1] += dtv * vxsph_y;
x[i][2] += dtv * vxsph_z;
} else {
// extrapolate velocity from half- to full-step
vest[i][0] = v[i][0] + dtfm * f[i][0];
vest[i][1] = v[i][1] + dtfm * f[i][1];
vest[i][2] = v[i][2] + dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixSMDIntegrateUlsph::final_integrate() {
double **v = atom->v;
double **f = atom->f;
double *e = atom->e;
double *de = atom->de;
double *vfrac = atom->vfrac;
double *radius = atom->radius;
double *contact_radius = atom->contact_radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup)
nlocal = atom->nfirst;
double dtfm, vsq, scale;
double *rmass = atom->rmass;
double vol_increment;
Matrix3d D;
/*
* get current number of SPH neighbors from ULSPH pair style
*/
int itmp;
int *nn = (int *) force->pair->extract("smd/ulsph/numNeighs_ptr", itmp);
if (nn == NULL) {
error->one(FLERR, "fix smd/integrate_ulsph failed to accesss num_neighs array");
}
Matrix3d *L = (Matrix3d *) force->pair->extract("smd/ulsph/velocityGradient_ptr", itmp);
if (L == NULL) {
error->one(FLERR, "fix smd/integrate_ulsph failed to accesss velocityGradient array");
}
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
if (vlimit > 0.0) {
vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
if (vsq > vlimitsq) {
scale = sqrt(vlimitsq / vsq);
v[i][0] *= scale;
v[i][1] *= scale;
v[i][2] *= scale;
}
}
e[i] += dtf * de[i];
if (adjust_radius_flag) {
if (nn[i] < min_nn) {
radius[i] *= adjust_radius_factor;
} else if (nn[i] > max_nn) {
radius[i] /= adjust_radius_factor;
}
radius[i] = MAX(radius[i], 1.25 * contact_radius[i]);
radius[i] = MIN(radius[i], 4.0 * contact_radius[i]);
}
D = 0.5 * (L[i] + L[i].transpose());
vol_increment = vfrac[i] * update->dt * D.trace(); // Jacobian of deformation
vfrac[i] += vol_increment;
}
}
}
/* ---------------------------------------------------------------------- */
void FixSMDIntegrateUlsph::reset_dt() {
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
}