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reformat modified core LAMMPS code

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This commit is contained in:
Axel Kohlmeyer
2019-09-24 14:36:44 -04:00
parent ed5407e998
commit 87d838d80b
2 changed files with 129 additions and 136 deletions
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230
src/fix_wall_reflect.cpp
View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@ -24,128 +24,121 @@
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixWallReflect::FixWallReflect(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
nwall(0)
{
{
if (narg < 4) error->all(FLERR,"Illegal fix wall/reflect command");
if (strcmp(arg[2],"wall/reflect") == 0){ // child class can be stochastic
if (strcmp(arg[2],"wall/reflect") == 0) { // child class can be stochastic
dynamic_group_allow = 1;
dynamic_group_allow = 1;
// parse args
// parse args
nwall = 0;
int scaleflag = 1;
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(FLERR,"Illegal fix wall/reflect command");
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(FLERR,"Illegal fix wall/reflect 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;
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 < 6); m++)
if (newwall == wallwhich[m])
error->all(FLERR,"Wall defined twice in fix wall/reflect command");
for (int m = 0; (m < nwall) && (m < 6); m++)
if (newwall == wallwhich[m])
error->all(FLERR,"Wall defined twice in fix wall/reflect 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] = force->numeric(FLERR,arg[iarg+1]);
}
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] = force->numeric(FLERR,arg[iarg+1]);
}
nwall++;
iarg += 2;
nwall++;
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal wall/reflect command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all(FLERR,"Illegal fix wall/reflect command");
iarg += 2;
} else error->all(FLERR,"Illegal fix wall/reflect command");
}
// error check
if (nwall == 0) error->all(FLERR,"Illegal fix wall command");
for (int m = 0; m < nwall; m++) {
if ((wallwhich[m] == XLO || wallwhich[m] == XHI) && domain->xperiodic)
error->all(FLERR,"Cannot use fix wall/reflect in periodic dimension");
if ((wallwhich[m] == YLO || wallwhich[m] == YHI) && domain->yperiodic)
error->all(FLERR,"Cannot use fix wall/reflect in periodic dimension");
if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->zperiodic)
error->all(FLERR,"Cannot use fix wall/reflect in periodic dimension");
}
for (int m = 0; m < nwall; m++)
if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->dimension == 2)
error->all(FLERR,
"Cannot use fix wall/reflect zlo/zhi for a 2d simulation");
// scale factors for CONSTANT and VARIABLE walls
int flag = 0;
for (int m = 0; m < nwall; m++)
if (wallstyle[m] != EDGE) flag = 1;
if (flag) {
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal wall/reflect command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all(FLERR,"Illegal fix wall/reflect command");
iarg += 2;
} else error->all(FLERR,"Illegal fix wall/reflect command");
}
else xscale = yscale = zscale = 1.0;
// error check
if (nwall == 0) error->all(FLERR,"Illegal fix wall command");
for (int m = 0; m < nwall; m++) {
if (wallstyle[m] != CONSTANT) continue;
if (wallwhich[m] < YLO) coord0[m] *= xscale;
else if (wallwhich[m] < ZLO) coord0[m] *= yscale;
else coord0[m] *= zscale;
if ((wallwhich[m] == XLO || wallwhich[m] == XHI) && domain->xperiodic)
error->all(FLERR,"Cannot use fix wall/reflect in periodic dimension");
if ((wallwhich[m] == YLO || wallwhich[m] == YHI) && domain->yperiodic)
error->all(FLERR,"Cannot use fix wall/reflect in periodic dimension");
if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->zperiodic)
error->all(FLERR,"Cannot use fix wall/reflect in periodic dimension");
}
for (int m = 0; m < nwall; m++)
if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->dimension == 2)
error->all(FLERR,
"Cannot use fix wall/reflect zlo/zhi for a 2d simulation");
// scale factors for CONSTANT and VARIABLE walls
int flag = 0;
for (int m = 0; m < nwall; m++)
if (wallstyle[m] != EDGE) flag = 1;
if (flag) {
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
for (int m = 0; m < nwall; m++) {
if (wallstyle[m] != CONSTANT) continue;
if (wallwhich[m] < YLO) coord0[m] *= xscale;
else if (wallwhich[m] < ZLO) coord0[m] *= yscale;
else coord0[m] *= zscale;
}
}
// set varflag if any wall positions are variable
varflag = 0;
for (int m = 0; m < nwall; m++)
if (wallstyle[m] == VARIABLE) varflag = 1;
}
// set varflag if any wall positions are variable
varflag = 0;
for (int m = 0; m < nwall; m++)
if (wallstyle[m] == VARIABLE) varflag = 1;
}
}
/* ---------------------------------------------------------------------- */
@ -200,8 +193,6 @@ void FixWallReflect::post_integrate()
// coord = current position of wall
// evaluate variable if necessary, wrap with clear/add
if (varflag) modify->clearstep_compute();
for (int m = 0; m < nwall; m++) {
@ -212,12 +203,10 @@ void FixWallReflect::post_integrate()
else coord *= zscale;
} else coord = coord0[m];
wall_particle(m,wallwhich[m],coord);
if (varflag) modify->addstep_compute(update->ntimestep + 1);
}
if (varflag) modify->addstep_compute(update->ntimestep + 1);
}
}
void FixWallReflect::wall_particle(int m, int which, double coord)
@ -229,22 +218,23 @@ void FixWallReflect::wall_particle(int m, int which, double coord)
int *mask = atom->mask;
int nlocal = atom->nlocal;
dim = which / 2;
side = which % 2;
dim = which / 2;
side = which % 2;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (side == 0) {
if (x[i][dim] < coord) {
x[i][dim] = coord + (coord - x[i][dim]);
v[i][dim] = -v[i][dim];
}
} else {
if (x[i][dim] > coord) {
x[i][dim] = coord - (x[i][dim] - coord);
v[i][dim] = -v[i][dim];
}
if (side == 0) {
if (x[i][dim] < coord) {
x[i][dim] = coord + (coord - x[i][dim]);
v[i][dim] = -v[i][dim];
}
} else {
if (x[i][dim] > coord) {
x[i][dim] = coord - (x[i][dim] - coord);
v[i][dim] = -v[i][dim];
}
}
}
}
}
}

35
src/random_mars.cpp
View File

@ -17,6 +17,7 @@
#include "random_mars.h"
#include <cmath>
#include "error.h"
#include "math_const.h"
using namespace LAMMPS_NS;
@ -122,10 +123,9 @@ double RanMars::gaussian()
double RanMars::gaussian(double mu, double sigma)
{
double v1;
v1 = mu+sigma*gaussian();
v1 = mu+sigma*gaussian();
return v1;
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
@ -136,13 +136,13 @@ double RanMars::rayleigh(double sigma)
{
double first,v1;
if (sigma <= 0)
if (sigma <= 0) {
error->all(FLERR,"Invalid Rayleigh parameter");
else {
} else {
v1 = uniform();
first = sigma*sqrt(-2.0*log(v1));
return first;
}
}
}
@ -153,17 +153,20 @@ double RanMars::rayleigh(double sigma)
double RanMars::besselexp(double theta, double alpha, double cp)
{
double first,v1,v2;
if ((theta < 0) || (alpha < 0) || (alpha >1))
if ((theta < 0) || (alpha < 0) || (alpha >1)) {
error->all(FLERR,"Invalid Bessel exponential distribution parameters");
else {
} else {
v1 = uniform();
v2 = uniform();
if (cp < 0)
first = sqrt((1-alpha)*cp*cp-2*alpha*theta*log(v1)+2*sqrt(-2*theta*(1-alpha)*alpha*log(v1))*cos(2*M_PI*v2)*cp);
else {
first = - sqrt((1-alpha)*cp*cp-2*alpha*theta*log(v1)-2*sqrt(-2*theta*(1-alpha)*alpha*log(v1))*cos(2*M_PI*v2)*cp) ;}
return first;
}
}
if (cp < 0) {
first = sqrt((1.0-alpha)*cp*cp - 2.0*alpha*theta*log(v1)
+ 2.0*sqrt(-2.0*theta*(1.0-alpha)*alpha*log(v1))
* cos(2.0*MathConst::MY_PI*v2)*cp);
} else {
first = -sqrt((1.0-alpha)*cp*cp - 2.0*alpha*theta*log(v1)
- 2.0*sqrt(-2.0*theta*(1.0-alpha)*alpha*log(v1))
* cos(2.0*MathConst::MY_PI*v2)*cp);
}
return first;
}
}