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changed potential file format to single file

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This commit is contained in:
Philipp Kloza
2020-01-13 22:52:52 +00:00
parent afcc1d935d
commit 2b51938a94
6 changed files with 1004113 additions and 1004118 deletions
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1004009
potentials/uSemi10x10.dat → potentials/10x10.cnt
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File diff suppressed because it is too large Load Diff

1002
potentials/gamma10x10.dat
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File diff suppressed because it is too large Load Diff

1002002
potentials/phi10x10.dat
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File diff suppressed because it is too large Load Diff

1002
potentials/uInf10x10.dat
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File diff suppressed because it is too large Load Diff

192
src/USER-MESOCNT/pair_mesocnt.cpp
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@ -42,13 +42,7 @@ using namespace MathExtra;
#define SELF_CUTOFF 20
#define SMALL 1.0e-6
#define SWITCH 1.0e-6
#define DELTA1 1.0
#define DELTA2 2.0
#define QUADRATURE 100
#define UINF_POINTS 1001
#define GAMMA_POINTS 26
#define PHI_POINTS 1001
#define USEMI_POINTS 1001
/* ---------------------------------------------------------------------- */
@ -445,25 +439,7 @@ void PairMesoCNT::allocate()
void PairMesoCNT::settings(int narg, char **arg)
{
if (narg == 0) {
uinf_points = UINF_POINTS;
gamma_points = GAMMA_POINTS;
phi_points = PHI_POINTS;
usemi_points = USEMI_POINTS;
}
else if (narg == 2) {
uinf_points = force->inumeric(FLERR,arg[0]);
gamma_points = force->inumeric(FLERR,arg[1]);
phi_points = force->inumeric(FLERR,arg[0]);
usemi_points = force->inumeric(FLERR,arg[0]);
}
else if (narg == 4) {
uinf_points = force->inumeric(FLERR,arg[0]);
gamma_points = force->inumeric(FLERR,arg[1]);
phi_points = force->inumeric(FLERR,arg[2]);
usemi_points = force->inumeric(FLERR,arg[3]);
}
else error->all(FLERR,"Illegal pair_style command");
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
@ -472,19 +448,11 @@ void PairMesoCNT::settings(int narg, char **arg)
void PairMesoCNT::coeff(int narg, char **arg)
{
if (narg != 8) error->all(FLERR,"Incorrect args for pair coefficients");
if (narg != 3) error->all(FLERR,"Incorrect args for pair coefficients");
file = arg[2];
read_file();
if (!allocated) allocate();
// CNT constants
n = force->inumeric(FLERR,arg[2]);
sig = force->numeric(FLERR,arg[3]);
// file names
uinf_file = arg[4];
gamma_file = arg[5];
phi_file = arg[6];
usemi_file = arg[7];
// units, eV to energy unit conversion
ang = force->angstrom;
ang_inv = 1.0 / ang;
@ -500,55 +468,18 @@ void PairMesoCNT::coeff(int narg, char **arg)
funit = eunit * ang_inv;
// potential variables
r = 1.421 * 3 * n / MY_2PI * ang;
sig = sig_ang * ang;
r = r_ang * ang;
rsq = r * r;
d = 2 * r;
d_ang = d * ang_inv;
d = 2.0 * r;
d_ang = 2.0 * r_ang;
rc = 3.0 * sig;
cutoff = rc + d;
cutoffsq = cutoff * cutoff;
cutoff_ang = cutoff * ang_inv;
cutoffsq_ang = cutoff_ang * cutoff_ang;
comega = 0.275 * (1.0 - 1.0/(1.0 + 0.59*r*ang_inv));
ctheta = 0.35 + 0.0226*(r*ang_inv - 6.785);
// parse and bcast data
int me;
double *uinf_data,*gamma_data,**phi_data,**usemi_data;
memory->create(uinf_data,uinf_points,"pair:uinf_data");
memory->create(gamma_data,gamma_points,"pair:gamma_data");
memory->create(phi_data,phi_points,phi_points,"pair:phi_data");
memory->create(usemi_data,usemi_points,phi_points,"pair:usemi_data");
MPI_Comm_rank(world,&me);
if (me == 0) {
read_file(uinf_file,uinf_data,hstart_uinf,delh_uinf,uinf_points);
read_file(gamma_file,gamma_data,hstart_gamma,delh_gamma,gamma_points);
read_file(phi_file,phi_data,hstart_phi,psistart_phi,
delh_phi,delpsi_phi,phi_points);
read_file(usemi_file,usemi_data,hstart_usemi,xistart_usemi,
delh_usemi,delxi_usemi,usemi_points);
}
MPI_Bcast(&hstart_uinf,1,MPI_DOUBLE,0,world);
MPI_Bcast(&hstart_gamma,1,MPI_DOUBLE,0,world);
MPI_Bcast(&hstart_phi,1,MPI_DOUBLE,0,world);
MPI_Bcast(&psistart_phi,1,MPI_DOUBLE,0,world);
MPI_Bcast(&hstart_usemi,1,MPI_DOUBLE,0,world);
MPI_Bcast(&xistart_usemi,1,MPI_DOUBLE,0,world);
MPI_Bcast(&delh_uinf,1,MPI_DOUBLE,0,world);
MPI_Bcast(&delh_gamma,1,MPI_DOUBLE,0,world);
MPI_Bcast(&delh_phi,1,MPI_DOUBLE,0,world);
MPI_Bcast(&delpsi_phi,1,MPI_DOUBLE,0,world);
MPI_Bcast(&delh_usemi,1,MPI_DOUBLE,0,world);
MPI_Bcast(&delxi_usemi,1,MPI_DOUBLE,0,world);
MPI_Bcast(uinf_data,uinf_points,MPI_DOUBLE,0,world);
MPI_Bcast(gamma_data,gamma_points,MPI_DOUBLE,0,world);
for (int i = 0; i < phi_points; i++)
MPI_Bcast(phi_data[i],phi_points,MPI_DOUBLE,0,world);
for (int i = 0; i < usemi_points; i++)
MPI_Bcast(usemi_data[i],usemi_points,MPI_DOUBLE,0,world);
comega = 0.275 * (1.0 - 1.0/(1.0 + 0.59*r_ang));
ctheta = 0.35 + 0.0226*(r_ang - 6.785);
// compute spline coefficients
spline_coeff(uinf_data,uinf_coeff,delh_uinf,uinf_points);
@ -811,17 +742,22 @@ void PairMesoCNT::sort(int *list, int size)
}
/* ----------------------------------------------------------------------
read 1D data file
read mesocnt potential file
------------------------------------------------------------------------- */
void PairMesoCNT::read_file(const char *file, double *data,
double &xstart, double &dx, int ninput)
void PairMesoCNT::read_file()
{
int me;
MPI_Comm_rank(world,&me);
FILE *fp;
if (me == 0) {
char line[MAXLINE];
// open file
FILE *fp = force->open_potential(file);
fp = force->open_potential(file);
if (fp == NULL) {
std::string str("Cannot open mesocnt file ");
str += file;
@ -829,6 +765,73 @@ void PairMesoCNT::read_file(const char *file, double *data,
}
fgets(line,MAXLINE,fp);
// potential parameters
fgets(line,MAXLINE,fp);
sscanf(line,"%d %d %d %d",
&uinf_points,&gamma_points,&phi_points,&usemi_points);
fgets(line,MAXLINE,fp);
sscanf(line,"%lg %lg %lg %lg",&r_ang,&sig_ang,&delta1,&delta2);
}
MPI_Bcast(&uinf_points,1,MPI_INT,0,world);
MPI_Bcast(&gamma_points,1,MPI_INT,0,world);
MPI_Bcast(&phi_points,1,MPI_INT,0,world);
MPI_Bcast(&usemi_points,1,MPI_INT,0,world);
MPI_Bcast(&r_ang,1,MPI_DOUBLE,0,world);
MPI_Bcast(&sig_ang,1,MPI_DOUBLE,0,world);
MPI_Bcast(&delta1,1,MPI_DOUBLE,0,world);
MPI_Bcast(&delta2,1,MPI_DOUBLE,0,world);
// potential tables
memory->create(uinf_data,uinf_points,"pair:uinf_data");
memory->create(gamma_data,gamma_points,"pair:gamma_data");
memory->create(phi_data,phi_points,phi_points,"pair:phi_data");
memory->create(usemi_data,usemi_points,phi_points,"pair:usemi_data");
if (me == 0) {
read_data(fp,uinf_data,hstart_uinf,delh_uinf,uinf_points);
read_data(fp,gamma_data,hstart_gamma,delh_gamma,gamma_points);
read_data(fp,phi_data,hstart_phi,psistart_phi,
delh_phi,delpsi_phi,phi_points);
read_data(fp,usemi_data,hstart_usemi,xistart_usemi,
delh_usemi,delxi_usemi,usemi_points);
fclose(fp);
}
MPI_Bcast(&hstart_uinf,1,MPI_DOUBLE,0,world);
MPI_Bcast(&hstart_gamma,1,MPI_DOUBLE,0,world);
MPI_Bcast(&hstart_phi,1,MPI_DOUBLE,0,world);
MPI_Bcast(&psistart_phi,1,MPI_DOUBLE,0,world);
MPI_Bcast(&hstart_usemi,1,MPI_DOUBLE,0,world);
MPI_Bcast(&xistart_usemi,1,MPI_DOUBLE,0,world);
MPI_Bcast(&delh_uinf,1,MPI_DOUBLE,0,world);
MPI_Bcast(&delh_gamma,1,MPI_DOUBLE,0,world);
MPI_Bcast(&delh_phi,1,MPI_DOUBLE,0,world);
MPI_Bcast(&delpsi_phi,1,MPI_DOUBLE,0,world);
MPI_Bcast(&delh_usemi,1,MPI_DOUBLE,0,world);
MPI_Bcast(&delxi_usemi,1,MPI_DOUBLE,0,world);
MPI_Bcast(uinf_data,uinf_points,MPI_DOUBLE,0,world);
MPI_Bcast(gamma_data,gamma_points,MPI_DOUBLE,0,world);
for (int i = 0; i < phi_points; i++)
MPI_Bcast(phi_data[i],phi_points,MPI_DOUBLE,0,world);
for (int i = 0; i < usemi_points; i++)
MPI_Bcast(usemi_data[i],usemi_points,MPI_DOUBLE,0,world);
}
/* ----------------------------------------------------------------------
read 1D data file
------------------------------------------------------------------------- */
void PairMesoCNT::read_data(FILE *fp, double *data,
double &xstart, double &dx, int ninput)
{
char line[MAXLINE];
fgets(line,MAXLINE,fp);
// read values from file
int cerror = 0;
@ -873,28 +876,17 @@ void PairMesoCNT::read_file(const char *file, double *data,
errstr += file;
error->warning(FLERR,errstr.c_str());
}
fclose(fp);
}
/* ----------------------------------------------------------------------
read 2D data file
------------------------------------------------------------------------- */
void PairMesoCNT::read_file(const char *file, double **data,
void PairMesoCNT::read_data(FILE *fp, double **data,
double &xstart, double &ystart,
double &dx, double &dy, int ninput)
{
char line[MAXLINE];
// open file
FILE *fp = force->open_potential(file);
if (fp == NULL) {
std::string str("Cannot open file ");
str += file;
error->one(FLERR,str.c_str());
}
fgets(line,MAXLINE,fp);
// read values from file
@ -959,8 +951,6 @@ void PairMesoCNT::read_file(const char *file, double **data,
errstr += file;
error->warning(FLERR,errstr.c_str());
}
fclose(fp);
}
/* ----------------------------------------------------------------------
@ -1654,9 +1644,9 @@ void PairMesoCNT::finf(const double *param, double &evdwl, double **f)
double zeta1 = xi1 * c1;
double zeta2 = xi2 * c1;
double smooth = s5((h-d_ang-DELTA1)/(DELTA2-DELTA1));
double dsmooth = ds5((h-d_ang-DELTA1)/(DELTA2-DELTA1));
double g = d_ang + DELTA2;
double smooth = s5((h-d_ang-delta1)/(delta2-delta1));
double dsmooth = ds5((h-d_ang-delta1)/(delta2-delta1));
double g = d_ang + delta2;
double hsq = h * h;
double zetaminbar;
@ -1669,7 +1659,7 @@ void PairMesoCNT::finf(const double *param, double &evdwl, double **f)
if (h >= g) dzetaminbar = 0;
else dzetaminbar = -h / zetaminbar;
double dzetamin =
dzetaminbar*smooth + zetaminbar*dsmooth/(DELTA2-DELTA1);
dzetaminbar*smooth + zetaminbar*dsmooth/(delta2-delta1);
double dzetamax = -h / zetamax;
double zeta_range_inv = 1.0 / (zetamax - zetamin);

12
src/USER-MESOCNT/pair_mesocnt.h
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@ -24,15 +24,15 @@ class PairMesoCNT : public Pair {
protected:
int uinf_points,gamma_points,phi_points,usemi_points;
int nlocal_size,reduced_neigh_size;
int n;
int *reduced_nlist,*numchainlist;
int **reduced_neighlist,**nchainlist,**endlist;
int ***chainlist;
double ang,ang_inv,eunit,funit;
double delta1,delta2;
double r,rsq,d,rc,rcsq,rc0,cutoff,cutoffsq;
double r_ang,rsq_ang,d_ang,rc_ang,rcsq_ang,cutoff_ang,cutoffsq_ang;
double sig,comega,ctheta;
double sig,sig_ang,comega,ctheta;
double hstart_uinf,hstart_gamma,
hstart_phi,psistart_phi,hstart_usemi,xistart_usemi;
double delh_uinf,delh_gamma,delh_phi,delpsi_phi,delh_usemi,delxi_usemi;
@ -41,18 +41,20 @@ class PairMesoCNT : public Pair {
double *param,*w,*wnode;
double **dq_w;
double ***q1_dq_w,***q2_dq_w;
double *uinf_data,*gamma_data,**phi_data,**usemi_data;
double **uinf_coeff,**gamma_coeff,****phi_coeff,****usemi_coeff;
double **flocal,**fglobal,**basis;
char *uinf_file,*gamma_file,*phi_file,*usemi_file;
char *file;
void allocate();
void bond_neigh();
void neigh_common(int, int, int &, int *);
void chain_split(int *, int, int &, int **, int *, int *);
void sort(int *, int);
void read_file(const char *, double *, double &, double &, int);
void read_file(const char *, double **, double &, double &,
void read_file();
void read_data(FILE *, double *, double &, double &, int);
void read_data(FILE *, double **, double &, double &,
double &, double &, int);
void spline_coeff(double *, double **, double, int);