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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5176 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2010-10-27 20:55:41 +00:00
parent 3ab35d6073
commit fcbd40ebf6
5 changed files with 1055 additions and 277 deletions
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4
src/SRD/Install.sh
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@ -3,13 +3,17 @@
if (test $1 == 1) then
cp fix_srd.cpp ..
cp fix_wall_srd.cpp ..
cp fix_srd.h ..
cp fix_wall_srd.h ..
elif (test $1 == 0) then
rm ../fix_srd.cpp
rm ../fix_wall_srd.cpp
rm ../fix_srd.h
rm ../fix_wall_srd.h
fi

976
src/SRD/fix_srd.cpp
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File diff suppressed because it is too large Load Diff

41
src/SRD/fix_srd.h
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@ -46,7 +46,7 @@ class FixSRD : public Fix {
int cubicflag,shiftuser,shiftseed,shiftflag,streamflag;
double gridsrd,gridsearch,lamda,radfactor,cubictol;
int triclinic,change_size,change_shape;
double dt_big,dt_srd;
double mass_big,mass_srd;
double temperature_srd;
@ -54,7 +54,14 @@ class FixSRD : public Fix {
double srd_per_cell;
double dmax,vmax,vmaxsq;
double maxbigdiam,minbigdiam;
double dist_bigghost;
double dist_ghost,dist_srd,dist_srd_reneigh; // explained in code
int wallexist,nwall,wallvarflag;
class FixWallSRD *wallfix;
int *wallwhich;
double *xwall,*xwallhold,*vwall;
double **fwall;
double walltrigger;
// for orthogonal box, these are in box units
// for triclinic box, these are in lamda units
@ -79,11 +86,11 @@ class FixSRD : public Fix {
double **flocal; // local ptrs to atom force and torque
double **tlocal;
// info to store for each owned and ghost big particle
// info to store for each owned and ghost big particle and wall
struct Big {
int index; // local index or particle in atom arrays
int type; // SPHERE or ELLIPSOID
int index; // local index of particle/wall
int type; // SPHERE or ELLIPSOID or WALL
int typesphere; // SPHERE_SHAPE or SPHERE_RADIUS
int typeangular; // ANGULAR_OMEGA or ANGULAR_ANGMOM
double radius,radsq; // radius of sphere
@ -95,15 +102,15 @@ class FixSRD : public Fix {
double ex[3],ey[3],ez[3]; // current orientation vecs for ellipsoid
};
Big *biglist; // list of info for each owned & ghost big particle
Big *biglist; // list of info for each owned & ghost big and wall
int any_ellipsoids; // 1 if any big particles are ellipsoids
int torqueflag; // 1 if any big particle is torqued
// current size of particle-based arrays
int nbig; // # of big particles, owned + ghost
int nmax;
int maxbig; // max number of big particles, owned + ghost
int nbig; // # of owned/ghost big particles and walls
int maxbig; // max number of owned/ghost big particles and walls
int nmax; // max number of SRD particles
// bins for SRD velocity remap, shifting and communication
// binsize and inv are in lamda units for triclinic
@ -170,6 +177,8 @@ class FixSRD : public Fix {
int inside_sphere(double *, double *, Big *);
int inside_ellipsoid(double *, double *, Big *);
int inside_wall(double *, int);
double collision_sphere_exact(double *, double *, double *, double *,
Big *, double *, double *, double *);
void collision_sphere_inexact(double *, double *,
@ -178,22 +187,34 @@ class FixSRD : public Fix {
Big *, double *, double *, double *);
void collision_ellipsoid_inexact(double *, double *,
Big *, double *, double *, double *);
double collision_wall_exact(double *, int, double *,
double *, double *, double *);
void collision_wall_inexact(double *, int, double *, double *, double *);
void slip_sphere(double *, double *, double *, double *);
void slip_ellipsoid(double *, double *, double *, Big *,
double *, double *, double *);
void slip_wall(double *, int, double *, double *);
void noslip(double *, double *, double *, Big *,
double *, double *, double *);
void noslip_wall(double *, int, double *, double *, double *);
void force_torque(double *, double *, double *,
double *, double *, double *);
void force_wall(double *, double *, int);
int update_srd(int, double, double *, double *, double *, double *);
void parameterize();
void setup_bounds();
void setup_velocity_bins();
void setup_velocity_shift(int, int);
void setup_search_bins();
void setup_search_stencil();
void big_static();
void big_dynamic();
double point_bin_distance(double *, int, int, int);
double bin_bin_distance(int, int, int);
void exyz_from_q(double *, double *, double *, double *);
@ -203,7 +224,7 @@ class FixSRD : public Fix {
double distance(int, int);
void print_collision(int, int, int, double, double,
double *, double *, double *);
double *, double *, double *, int);
};
}

252
src/SRD/fix_wall_srd.cpp Normal file
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@ -0,0 +1,252 @@
/* ----------------------------------------------------------------------
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 "stdlib.h"
#include "string.h"
#include "fix_wall_srd.h"
#include "atom.h"
#include "modify.h"
#include "fix.h"
#include "domain.h"
#include "lattice.h"
#include "input.h"
#include "modify.h"
#include "update.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{XLO,XHI,YLO,YHI,ZLO,ZHI};
enum{NONE,EDGE,CONSTANT,VARIABLE};
/* ---------------------------------------------------------------------- */
FixWallSRD::FixWallSRD(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 4) error->all("Illegal fix wall/srd command");
// parse args
nwall = 0;
int scaleflag = 1;
int iarg = 3;
while (iarg < narg) {
if ((strcmp(arg[iarg],"xlo") == 0) || (strcmp(arg[iarg],"xhi") == 0) ||
(strcmp(arg[iarg],"ylo") == 0) || (strcmp(arg[iarg],"yhi") == 0) ||
(strcmp(arg[iarg],"zlo") == 0) || (strcmp(arg[iarg],"zhi") == 0)) {
if (iarg+2 > narg) error->all("Illegal fix wall/srd command");
int newwall;
if (strcmp(arg[iarg],"xlo") == 0) newwall = XLO;
else if (strcmp(arg[iarg],"xhi") == 0) newwall = XHI;
else if (strcmp(arg[iarg],"ylo") == 0) newwall = YLO;
else if (strcmp(arg[iarg],"yhi") == 0) newwall = YHI;
else if (strcmp(arg[iarg],"zlo") == 0) newwall = ZLO;
else if (strcmp(arg[iarg],"zhi") == 0) newwall = ZHI;
for (int m = 0; m < nwall; m++)
if (newwall == wallwhich[m])
error->all("Wall defined twice in fix wall/srd command");
wallwhich[nwall] = newwall;
if (strcmp(arg[iarg+1],"EDGE") == 0) {
wallstyle[nwall] = EDGE;
int dim = wallwhich[nwall] / 2;
int side = wallwhich[nwall] % 2;
if (side == 0) coord0[nwall] = domain->boxlo[dim];
else coord0[nwall] = domain->boxhi[dim];
} else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
wallstyle[nwall] = VARIABLE;
int n = strlen(&arg[iarg+1][2]) + 1;
varstr[nwall] = new char[n];
strcpy(varstr[nwall],&arg[iarg+1][2]);
} else {
wallstyle[nwall] = CONSTANT;
coord0[nwall] = atof(arg[iarg+1]);
}
nwall++;
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all("Illegal wall/srd command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all("Illegal fix wall/srd command");
iarg += 2;
} else error->all("Illegal fix wall/srd command");
}
// error check
if (nwall == 0) error->all("Illegal fix wall command");
for (int m = 0; m < nwall; m++) {
if ((wallwhich[m] == XLO || wallwhich[m] == XHI) && domain->xperiodic)
error->all("Cannot use fix wall/srd in periodic dimension");
if ((wallwhich[m] == YLO || wallwhich[m] == YHI) && domain->yperiodic)
error->all("Cannot use fix wall/srd in periodic dimension");
if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->zperiodic)
error->all("Cannot use fix wall/srd in periodic dimension");
}
for (int m = 0; m < nwall; m++)
if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->dimension == 2)
error->all("Cannot use fix wall/srd zlo/zhi for a 2d simulation");
// setup wall force array
array_flag = 1;
size_array_rows = nwall;
size_array_cols = 3;
global_freq = 1;
extarray = 1;
fwall = memory->create_2d_double_array(nwall,3,"wall/srd:fwall");
fwall_all = memory->create_2d_double_array(nwall,3,"wall/srd:fwall_all");
// scale coord for CONSTANT walls
int flag = 0;
for (int m = 0; m < nwall; m++)
if (wallstyle[m] == CONSTANT) flag = 1;
if (flag) {
if (scaleflag && domain->lattice == NULL)
error->all("Use of fix wall with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
double scale;
for (int m = 0; m < nwall; m++) {
if (wallwhich[m] < YLO) scale = xscale;
else if (wallwhich[m] < ZLO) scale = yscale;
else scale = zscale;
if (wallstyle[m] == CONSTANT) coord0[m] *= scale;
}
}
// set time_depend and varflag if any wall positions are variable
varflag = 0;
for (int m = 0; m < nwall; m++)
if (wallstyle[m] == VARIABLE) time_depend = varflag = 1;
laststep = -1;
}
/* ---------------------------------------------------------------------- */
FixWallSRD::~FixWallSRD()
{
for (int m = 0; m < nwall; m++)
if (wallstyle[m] == VARIABLE) delete [] varstr[m];
memory->destroy_2d_double_array(fwall);
memory->destroy_2d_double_array(fwall_all);
}
/* ---------------------------------------------------------------------- */
int FixWallSRD::setmask()
{
int mask = 0;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixWallSRD::init()
{
int flag = 0;
for (int m = 0; m < modify->nfix; m++)
if (strcmp(modify->fix[m]->style,"srd2") == 0) flag = 1;
if (!flag) error->all("Cannot use fix wall/srd without fix srd");
for (int m = 0; m < nwall; m++) {
if (wallstyle[m] != VARIABLE) continue;
varindex[m] = input->variable->find(varstr[m]);
if (varindex[m] < 0)
error->all("Variable name for fix wall/srd does not exist");
if (!input->variable->equalstyle(varindex[m]))
error->all("Variable for fix wall/srd is invalid style");
}
dt = update->dt;
}
/* ----------------------------------------------------------------------
return force component on a wall
------------------------------------------------------------------------- */
double FixWallSRD::compute_array(int i, int j)
{
// only sum across procs one time
if (force_flag == 0) {
MPI_Allreduce(&fwall[0][0],&fwall_all[0][0],3*nwall,
MPI_DOUBLE,MPI_SUM,world);
force_flag = 1;
}
return fwall_all[i][j];
}
/* ----------------------------------------------------------------------
set wall position and velocity, zero forces on walls
evaluate variable if necessary, wrap with clear/add
if flag, then being called on reneighbor, so archive wall positions
------------------------------------------------------------------------- */
void FixWallSRD::wall_params(int flag)
{
double xnew;
if (varflag) modify->clearstep_compute();
int ntimestep = update->ntimestep;
for (int m = 0; m < nwall; m++) {
if (wallstyle[m] == VARIABLE)
xnew = input->variable->compute_equal(varindex[m]);
else xnew = coord0[m];
if (laststep < 0) {
xwall[m] = xwalllast[m] = xnew;
vwall[m] = 0.0;
} else if (laststep < ntimestep) {
xwalllast[m] = xwall[m];
xwall[m] = xnew;
vwall[m] = (xwall[m] - xwalllast[m]) / dt;
}
fwall[m][0] = fwall[m][1] = fwall[m][2] = 0.0;
}
laststep = ntimestep;
if (varflag) modify->addstep_compute(update->ntimestep + 1);
if (flag)
for (int m = 0; m < nwall; m++)
xwallhold[m] = xwall[m];
force_flag = 0;
}

59
src/SRD/fix_wall_srd.h Normal file
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@ -0,0 +1,59 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(wall/srd,FixWallSRD)
#else
#ifndef LMP_FIX_WALL_SRD_H
#define LMP_FIX_WALL_SRD_H
#include "fix.h"
namespace LAMMPS_NS {
class FixWallSRD : public Fix {
public:
int nwall,varflag;
int wallwhich[6];
double xwall[6],xwallhold[6],vwall[6];
double **fwall;
FixWallSRD(class LAMMPS *, int, char **);
~FixWallSRD();
int setmask();
void init();
double compute_array(int, int);
void wall_params(int);
private:
int wallstyle[6];
double coord0[6];
char *varstr[6];
int varindex[6];
double dt;
double xwalllast[6];
int laststep;
double **fwall_all;
int force_flag;
};
}
#endif
#endif