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pair_smd_triangulated_surface.cpp
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pair_smd_triangulated_surface.cpp
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/* ----------------------------------------------------------------------
*
* *** 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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <float.h>
#include <stdlib.h>
#include <string.h>
#include "pair_smd_triangulated_surface.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include <Eigen/Eigen>
#include <stdio.h>
#include <iostream>
using namespace std;
using namespace LAMMPS_NS;
using namespace Eigen;
#define SQRT2 1.414213562e0
/* ---------------------------------------------------------------------- */
PairTriSurf::PairTriSurf(LAMMPS *lmp) :
Pair(lmp) {
onerad_dynamic = onerad_frozen = maxrad_dynamic = maxrad_frozen = NULL;
bulkmodulus = NULL;
kn = NULL;
scale = 1.0;
}
/* ---------------------------------------------------------------------- */
PairTriSurf::~PairTriSurf() {
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(bulkmodulus);
memory->destroy(kn);
delete[] onerad_dynamic;
delete[] onerad_frozen;
delete[] maxrad_dynamic;
delete[] maxrad_frozen;
}
}
/* ---------------------------------------------------------------------- */
void PairTriSurf::compute(int eflag, int vflag) {
int i, j, ii, jj, inum, jnum, itype, jtype;
double rsq, r, evdwl, fpair;
int *ilist, *jlist, *numneigh, **firstneigh;
double rcut, r_geom, delta, r_tri, r_particle, touch_distance, dt_crit;
int tri, particle;
Vector3d normal, x1, x2, x3, x4, x13, x23, x43, w, cp, x4cp, vnew, v_old;
;
Vector3d xi, x_center, dx;
Matrix2d C;
Vector2d w2d, rhs;
evdwl = 0.0;
if (eflag || vflag)
ev_setup(eflag, vflag);
else
evflag = vflag_fdotr = 0;
tagint *mol = atom->molecule;
double **f = atom->f;
double **smd_data_9 = atom->smd_data_9;
double **x = atom->x;
double **x0 = atom->x0;
double **v = atom->v;
double *rmass = atom->rmass;
int *type = atom->type;
int nlocal = atom->nlocal;
double *radius = atom->contact_radius;
double rcutSq;
Vector3d offset;
int newton_pair = force->newton_pair;
int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
int max_neighs = 0;
stable_time_increment = 1.0e22;
// loop over neighbors of my atoms using a half neighbor list
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
max_neighs = MAX(max_neighs, jnum);
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
/*
* decide which one of i, j is triangle and which is particle
*/
if ((mol[i] < 65535) && (mol[j] >= 65535)) {
particle = i;
tri = j;
} else if ((mol[j] < 65535) && (mol[i] >= 65535)) {
particle = j;
tri = i;
} else {
error->one(FLERR, "unknown case");
}
//x_center << x[tri][0], x[tri][1], x[tri][2]; // center of triangle
x_center(0) = x[tri][0];
x_center(1) = x[tri][1];
x_center(2) = x[tri][2];
//x4 << x[particle][0], x[particle][1], x[particle][2];
x4(0) = x[particle][0];
x4(1) = x[particle][1];
x4(2) = x[particle][2];
dx = x_center - x4; //
if (periodic) {
domain->minimum_image(dx(0), dx(1), dx(2));
}
rsq = dx.squaredNorm();
r_tri = scale * radius[tri];
r_particle = scale * radius[particle];
rcut = r_tri + r_particle;
rcutSq = rcut * rcut;
//printf("type i=%d, type j=%d, r=%f, ri=%f, rj=%f\n", itype, jtype, sqrt(rsq), ri, rj);
if (rsq < rcutSq) {
/*
* gather triangle information
*/
normal(0) = x0[tri][0];
normal(1) = x0[tri][1];
normal(2) = x0[tri][2];
/*
* distance check: is particle closer than its radius to the triangle plane?
*/
if (fabs(dx.dot(normal)) < radius[particle]) {
/*
* get other two triangle vertices
*/
x1(0) = smd_data_9[tri][0];
x1(1) = smd_data_9[tri][1];
x1(2) = smd_data_9[tri][2];
x2(0) = smd_data_9[tri][3];
x2(1) = smd_data_9[tri][4];
x2(2) = smd_data_9[tri][5];
x3(0) = smd_data_9[tri][6];
x3(1) = smd_data_9[tri][7];
x3(2) = smd_data_9[tri][8];
PointTriangleDistance(x4, x1, x2, x3, cp, r);
/*
* distance to closest point
*/
x4cp = x4 - cp;
/*
* flip normal to point in direction of x4cp
*/
if (x4cp.dot(normal) < 0.0) {
normal *= -1.0;
}
/*
* penalty force pushes particle away from triangle
*/
if (r < 1.0 * radius[particle]) {
delta = radius[particle] - r; // overlap distance
r_geom = radius[particle];
fpair = 1.066666667e0 * bulkmodulus[itype][jtype] * delta * sqrt(delta * r_geom);
dt_crit = 3.14 * sqrt(rmass[particle] / (fpair / delta));
stable_time_increment = MIN(stable_time_increment, dt_crit);
evdwl = r * fpair * 0.4e0 * delta; // GCG 25 April: this expression conserves total energy
fpair /= (r + 1.0e-2 * radius[particle]); // divide by r + softening and multiply with non-normalized distance vector
if (particle < nlocal) {
f[particle][0] += x4cp(0) * fpair;
f[particle][1] += x4cp(1) * fpair;
f[particle][2] += x4cp(2) * fpair;
}
if (tri < nlocal) {
f[tri][0] -= x4cp(0) * fpair;
f[tri][1] -= x4cp(1) * fpair;
f[tri][2] -= x4cp(2) * fpair;
}
if (evflag) {
ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, x4cp(0), x4cp(1), x4cp(2));
}
}
/*
* if particle comes too close to triangle, reflect its velocity and explicitely move it away
*/
touch_distance = 1.0 * radius[particle];
if (r < touch_distance) {
/*
* reflect velocity if it points toward triangle
*/
normal = x4cp / r;
//v_old << v[particle][0], v[particle][1], v[particle][2];
v_old(0) = v[particle][0];
v_old(1) = v[particle][1];
v_old(2) = v[particle][2];
if (v_old.dot(normal) < 0.0) {
//printf("flipping velocity\n");
vnew = 1.0 * (-2.0 * v_old.dot(normal) * normal + v_old);
v[particle][0] = vnew(0);
v[particle][1] = vnew(1);
v[particle][2] = vnew(2);
}
//printf("moving particle on top of triangle\n");
x[particle][0] = cp(0) + touch_distance * normal(0);
x[particle][1] = cp(1) + touch_distance * normal(1);
x[particle][2] = cp(2) + touch_distance * normal(2);
}
}
}
}
}
// int max_neighs_all = 0;
// MPI_Allreduce(&max_neighs, &max_neighs_all, 1, MPI_INT, MPI_MAX, world);
// if (comm->me == 0) {
// printf("max. neighs in tri pair is %d\n", max_neighs_all);
// }
//
// double stable_time_increment_all = 0.0;
// MPI_Allreduce(&stable_time_increment, &stable_time_increment_all, 1, MPI_DOUBLE, MPI_MIN, world);
// if (comm->me == 0) {
// printf("stable time step tri pair is %f\n", stable_time_increment_all);
// }
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairTriSurf::allocate() {
allocated = 1;
int n = atom->ntypes;
memory->create(setflag, n + 1, n + 1, "pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(bulkmodulus, n + 1, n + 1, "pair:kspring");
memory->create(kn, n + 1, n + 1, "pair:kn");
memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); // always needs to be allocated, even with granular neighborlist
onerad_dynamic = new double[n + 1];
onerad_frozen = new double[n + 1];
maxrad_dynamic = new double[n + 1];
maxrad_frozen = new double[n + 1];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairTriSurf::settings(int narg, char **arg) {
if (narg != 1)
error->all(FLERR, "Illegal number of args for pair_style smd/tri_surface");
scale = force->numeric(FLERR, arg[0]);
if (comm->me == 0) {
printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
printf("SMD/TRI_SURFACE CONTACT SETTINGS:\n");
printf("... effective contact radius is scaled by %f\n", scale);
printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairTriSurf::coeff(int narg, char **arg) {
if (narg != 3)
error->all(FLERR, "Incorrect args for pair coefficients");
if (!allocated)
allocate();
int ilo, ihi, jlo, jhi;
force->bounds(arg[0], atom->ntypes, ilo, ihi);
force->bounds(arg[1], atom->ntypes, jlo, jhi);
double bulkmodulus_one = atof(arg[2]);
// set short-range force constant
double kn_one = 0.0;
if (domain->dimension == 3) {
kn_one = (16. / 15.) * bulkmodulus_one; //assuming poisson ratio = 1/4 for 3d
} else {
kn_one = 0.251856195 * (2. / 3.) * bulkmodulus_one; //assuming poisson ratio = 1/3 for 2d
}
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo, i); j <= jhi; j++) {
bulkmodulus[i][j] = bulkmodulus_one;
kn[i][j] = kn_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0)
error->all(FLERR, "Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairTriSurf::init_one(int i, int j) {
if (!allocated)
allocate();
if (setflag[i][j] == 0)
error->all(FLERR, "All pair coeffs are not set");
bulkmodulus[j][i] = bulkmodulus[i][j];
kn[j][i] = kn[i][j];
// cutoff = sum of max I,J radii for
// dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen
double cutoff = maxrad_dynamic[i] + maxrad_dynamic[j];
cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]);
cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]);
if (comm->me == 0) {
printf("cutoff for pair smd/smd/tri_surface = %f\n", cutoff);
}
return cutoff;
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairTriSurf::init_style() {
int i;
// error checks
if (!atom->contact_radius_flag)
error->all(FLERR, "Pair style smd/smd/tri_surface requires atom style with contact_radius");
// old: half list
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->gran = 1;
// need a full neighbor list
// int irequest = neighbor->request(this);
// neighbor->requests[irequest]->half = 0;
// neighbor->requests[irequest]->full = 1;
// set maxrad_dynamic and maxrad_frozen for each type
// include future Fix pour particles as dynamic
for (i = 1; i <= atom->ntypes; i++)
onerad_dynamic[i] = onerad_frozen[i] = 0.0;
double *radius = atom->radius;
int *type = atom->type;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]);
}
MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
optional granular history list
------------------------------------------------------------------------- */
void PairTriSurf::init_list(int id, NeighList *ptr) {
if (id == 0)
list = ptr;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairTriSurf::memory_usage() {
return 0.0;
}
/*
* distance between triangle and point
*/
/*
function [dist,PP0] = pointTriangleDistance(TRI,P)
% calculate distance between a point and a triangle in 3D
% SYNTAX
% dist = pointTriangleDistance(TRI,P)
% [dist,PP0] = pointTriangleDistance(TRI,P)
%
% DESCRIPTION
% Calculate the distance of a given point P from a triangle TRI.
% Point P is a row vector of the form 1x3. The triangle is a matrix
% formed by three rows of points TRI = [P1;P2;P3] each of size 1x3.
% dist = pointTriangleDistance(TRI,P) returns the distance of the point P
% to the triangle TRI.
% [dist,PP0] = pointTriangleDistance(TRI,P) additionally returns the
% closest point PP0 to P on the triangle TRI.
%
% Author: Gwendolyn Fischer
% Release: 1.0
% Release date: 09/02/02
% Release: 1.1 Fixed Bug because of normalization
% Release: 1.2 Fixed Bug because of typo in region 5 20101013
% Release: 1.3 Fixed Bug because of typo in region 2 20101014
% Possible extention could be a version tailored not to return the distance
% and additionally the closest point, but instead return only the closest
% point. Could lead to a small speed gain.
% Example:
% %% The Problem
% P0 = [0.5 -0.3 0.5];
%
% P1 = [0 -1 0];
% P2 = [1 0 0];
% P3 = [0 0 0];
%
% vertices = [P1; P2; P3];
% faces = [1 2 3];
%
% %% The Engine
% [dist,PP0] = pointTriangleDistance([P1;P2;P3],P0);
%
% %% Visualization
% [x,y,z] = sphere(20);
% x = dist*x+P0(1);
% y = dist*y+P0(2);
% z = dist*z+P0(3);
%
% figure
% hold all
% patch('Vertices',vertices,'Faces',faces,'FaceColor','r','FaceAlpha',0.8);
% plot3(P0(1),P0(2),P0(3),'b*');
% plot3(PP0(1),PP0(2),PP0(3),'*g')
% surf(x,y,z,'FaceColor','b','FaceAlpha',0.3)
% view(3)
% The algorithm is based on
% "David Eberly, 'Distance Between Point and Triangle in 3D',
% Geometric Tools, LLC, (1999)"
% http:\\www.geometrictools.com/Documentation/DistancePoint3Triangle3.pdf
%
% ^t
% \ |
% \reg2|
% \ |
% \ |
% \ |
% \|
% *P2
% |\
% | \
% reg3 | \ reg1
% | \
% |reg0\
% | \
% | \ P1
% -------*-------*------->s
% |P0 \
% reg4 | reg5 \ reg6
*/
//void PairTriSurf::PointTriangleDistance(const Vector3d P, const Vector3d TRI1, const Vector3d TRI2, const Vector3d TRI3,
// Vector3d &CP, double &dist) {
//
// Vector3d B, E0, E1, D;
// double a, b, c, d, e, f;
// double det, s, t, sqrDistance, tmp0, tmp1, numer, denom, invDet;
//
// // rewrite triangle in normal form
// B = TRI1;
// E0 = TRI2 - B;
// E1 = TRI3 - B;
//
// D = B - P;
// a = E0.dot(E0);
// b = E0.dot(E1);
// c = E1.dot(E1);
// d = E0.dot(D);
// e = E1.dot(D);
// f = D.dot(D);
//
// det = a * c - b * b;
// //% do we have to use abs here?
// s = b * e - c * d;
// t = b * d - a * e;
//
// //% Terible tree of conditionals to determine in which region of the diagram
// //% shown above the projection of the point into the triangle-plane lies.
// if ((s + t) <= det) {
// if (s < 0) {
// if (t < 0) {
// // %region4
// if (d < 0) {
// t = 0;
// if (-d >= a) {
// s = 1;
// sqrDistance = a + 2 * d + f;
// } else {
// s = -d / a;
// sqrDistance = d * s + f;
// }
// } else {
// s = 0;
// if (e >= 0) {
// t = 0;
// sqrDistance = f;
// } else {
// if (-e >= c) {
// t = 1;
// sqrDistance = c + 2 * e + f;
// } else {
// t = -e / c;
// sqrDistance = e * t + f;
// }
// }
// }
// // end % of region 4
// } else {
// // % region 3
// s = 0;
// if (e >= 0) {
// t = 0;
// sqrDistance = f;
// } else {
// if (-e >= c) {
// t = 1;
// sqrDistance = c + 2 * e + f;
// } else {
// t = -e / c;
// sqrDistance = e * t + f;
// }
// }
// }
// // end of region 3
// } else {
// if (t < 0) {
// //% region 5
// t = 0;
// if (d >= 0) {
// s = 0;
// sqrDistance = f;
// } else {
// if (-d >= a) {
// s = 1;
// sqrDistance = a + 2 * d + f;
// } else {
// s = -d / a;
// sqrDistance = d * s + f;
// }
// }
// } else {
// // region 0
// invDet = 1 / det;
// s = s * invDet;
// t = t * invDet;
// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f;
// }
// }
// } else {
// if (s < 0) {
// // % region 2
// tmp0 = b + d;
// tmp1 = c + e;
// if (tmp1 > tmp0) { //% minimum on edge s+t=1
// numer = tmp1 - tmp0;
// denom = a - 2 * b + c;
// if (numer >= denom) {
// s = 1;
// t = 0;
// sqrDistance = a + 2 * d + f;
// } else {
// s = numer / denom;
// t = 1 - s;
// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f;
// }
// } else
// // % minimum on edge s=0
// s = 0;
// if (tmp1 <= 0) {
// t = 1;
// sqrDistance = c + 2 * e + f;
// } else {
// if (e >= 0) {
// t = 0;
// sqrDistance = f;
// } else {
// t = -e / c;
// sqrDistance = e * t + f;
// }
// }
// } //end % of region 2
// else {
// if (t < 0) {
// // %region6
// tmp0 = b + e;
// tmp1 = a + d;
// if (tmp1 > tmp0) {
// numer = tmp1 - tmp0;
// denom = a - 2 * b + c;
// if (numer >= denom) {
// t = 1;
// s = 0;
// sqrDistance = c + 2 * e + f;
// } else {
// t = numer / denom;
// s = 1 - t;
// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f;
// }
// } else {
// t = 0;
// if (tmp1 <= 0) {
// s = 1;
// sqrDistance = a + 2 * d + f;
// } else {
// if (d >= 0) {
// s = 0;
// sqrDistance = f;
// } else {
// s = -d / a;
// sqrDistance = d * s + f;
// }
// }
// } // % end region 6
// } else {
// //% region 1
// numer = c + e - b - d;
// if (numer <= 0) {
// s = 0;
// t = 1;
// sqrDistance = c + 2 * e + f;
// } else {
// denom = a - 2 * b + c;
// if (numer >= denom) {
// s = 1;
// t = 0;
// sqrDistance = a + 2 * d + f;
// } else {
// s = numer / denom;
// t = 1 - s;
// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f;
// }
// } //% end of region 1
// }
// }
// }
//
// // % account for numerical round-off error
// if (sqrDistance < 0) {
// sqrDistance = 0;
// }
//
// dist = sqrt(sqrDistance);
//
// // closest point
// CP = B + s * E0 + t * E1;
//
//}
/*
* % The algorithm is based on
% "David Eberly, 'Distance Between Point and Triangle in 3D',
% Geometric Tools, LLC, (1999)"
% http:\\www.geometrictools.com/Documentation/DistancePoint3Triangle3.pdf
*/
void PairTriSurf::PointTriangleDistance(const Vector3d sourcePosition, const Vector3d TRI0, const Vector3d TRI1,
const Vector3d TRI2, Vector3d &CP, double &dist) {
Vector3d edge0 = TRI1 - TRI0;
Vector3d edge1 = TRI2 - TRI0;
Vector3d v0 = TRI0 - sourcePosition;
double a = edge0.dot(edge0);
double b = edge0.dot(edge1);
double c = edge1.dot(edge1);
double d = edge0.dot(v0);
double e = edge1.dot(v0);
double det = a * c - b * b;
double s = b * e - c * d;
double t = b * d - a * e;
if (s + t < det) {
if (s < 0.f) {
if (t < 0.f) {
if (d < 0.f) {
s = clamp(-d / a, 0.f, 1.f);
t = 0.f;
} else {
s = 0.f;
t = clamp(-e / c, 0.f, 1.f);
}
} else {
s = 0.f;
t = clamp(-e / c, 0.f, 1.f);
}
} else if (t < 0.f) {
s = clamp(-d / a, 0.f, 1.f);
t = 0.f;
} else {
float invDet = 1.f / det;
s *= invDet;
t *= invDet;
}
} else {
if (s < 0.f) {
float tmp0 = b + d;
float tmp1 = c + e;
if (tmp1 > tmp0) {
float numer = tmp1 - tmp0;
float denom = a - 2 * b + c;
s = clamp(numer / denom, 0.f, 1.f);
t = 1 - s;
} else {
t = clamp(-e / c, 0.f, 1.f);
s = 0.f;
}
} else if (t < 0.f) {
if (a + d > b + e) {
float numer = c + e - b - d;
float denom = a - 2 * b + c;
s = clamp(numer / denom, 0.f, 1.f);
t = 1 - s;
} else {
s = clamp(-e / c, 0.f, 1.f);
t = 0.f;
}
} else {
float numer = c + e - b - d;
float denom = a - 2 * b + c;
s = clamp(numer / denom, 0.f, 1.f);
t = 1.f - s;
}
}
CP = TRI0 + s * edge0 + t * edge1;
dist = (CP - sourcePosition).norm();
}
double PairTriSurf::clamp(const double a, const double min, const double max) {
if (a < min) {
return min;
} else if (a > max) {
return max;
} else {
return a;
}
}
void *PairTriSurf::extract(const char *str, int &i) {
//printf("in PairTriSurf::extract\n");
if (strcmp(str, "smd/tri_surface/stable_time_increment_ptr") == 0) {
return (void *) &stable_time_increment;
}
return NULL;
}

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