jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3598 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-12-21 21:21:22 +00:00
parent 87ba3c6eff
commit 4900c3d0c0
14 changed files with 57 additions and 66 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
src/XTC/dump_xtc.cpp
View File

@ -229,18 +229,18 @@ int DumpXTC::pack()
/* ---------------------------------------------------------------------- */
void DumpXTC::write_data(int n, double *buf)
void DumpXTC::write_data(int n, double *mybuf)
{
float *xyz;
int j,tag;
int m = 0;
for (int i = 0; i < n; i++) {
tag = static_cast<int> (buf[m]) - 1;
tag = static_cast<int> (mybuf[m]) - 1;
j = 3*tag;
coords[j++] = buf[m+1];
coords[j++] = buf[m+2];
coords[j] = buf[m+3];
coords[j++] = mybuf[m+1];
coords[j++] = mybuf[m+2];
coords[j] = mybuf[m+3];
m += size_one;
}

2
src/compute_com_molecule.cpp
View File

@ -150,7 +150,7 @@ void ComputeCOMMolecule::compute_array()
double ComputeCOMMolecule::memory_usage()
{
double bytes = 2*nmolecules * sizeof(double);
if (molmap) bytes += nmolecules * sizeof(int);
if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
bytes += 2*nmolecules*3 * sizeof(double);
return bytes;
}

2
src/compute_gyration_molecule.cpp
View File

@ -180,7 +180,7 @@ void ComputeGyrationMolecule::compute_vector()
double ComputeGyrationMolecule::memory_usage()
{
double bytes = 4*nmolecules * sizeof(double);
if (molmap) bytes += nmolecules * sizeof(int);
if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
bytes += 2*nmolecules*3 * sizeof(double);
return bytes;
}

27
src/compute_msd.cpp
View File

@ -118,6 +118,7 @@ void ComputeMSD::compute_vector()
double cm[3];
if (comflag) group->xcm(igroup,masstotal,cm);
else cm[0] = cm[1] = cm[2] = 0.0;
// dx,dy,dz = displacement of atom from original position
// original unwrapped position is stored by fix
@ -148,15 +149,9 @@ void ComputeMSD::compute_vector()
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
if (comflag) {
dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0];
dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1];
dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2];
} else {
dx = x[i][0] + xbox*xprd - xoriginal[i][0];
dy = x[i][1] + ybox*yprd - xoriginal[i][1];
dz = x[i][2] + zbox*zprd - xoriginal[i][2];
}
dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0];
dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1];
dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2];
msd[0] += dx*dx;
msd[1] += dy*dy;
msd[2] += dz*dz;
@ -169,16 +164,10 @@ void ComputeMSD::compute_vector()
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
if (comflag) {
dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox -
cm[0] - xoriginal[i][0];
dy = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1] - xoriginal[i][1];
dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2];
} else {
dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0];
dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1];
dz = x[i][2] + h[2]*zbox - xoriginal[i][2];
}
dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox -
cm[0] - xoriginal[i][0];
dy = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1] - xoriginal[i][1];
dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2];
msd[0] += dx*dx;
msd[1] += dy*dy;
msd[2] += dz*dz;

2
src/compute_msd_molecule.cpp
View File

@ -183,7 +183,7 @@ void ComputeMSDMolecule::compute_array()
double ComputeMSDMolecule::memory_usage()
{
double bytes = 2*nmolecules * sizeof(double);
if (molmap) bytes += nmolecules * sizeof(int);
if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
bytes += 2*nmolecules*3 * sizeof(double);
bytes += nmolecules*4 * sizeof(double);
return bytes;

2
src/compute_property_atom.cpp
View File

@ -249,7 +249,7 @@ void ComputePropertyAtom::compute_peratom()
buf = vector;
(this->*pack_choice[0])(0);
} else {
if (array) buf = array[0];
if (array) buf = &array[0][0];
for (int n = 0; n < nvalues; n++)
(this->*pack_choice[n])(n);
}

2
src/compute_property_local.cpp
View File

@ -216,7 +216,7 @@ void ComputePropertyLocal::compute_local()
buf = vector;
(this->*pack_choice[0])(0);
} else {
if (array) buf = array[0];
if (array) buf = &array[0][0];
for (int n = 0; n < nvalues; n++)
(this->*pack_choice[n])(n);
}

22
src/dump_atom.cpp
View File

@ -153,9 +153,9 @@ int DumpAtom::pack()
/* ---------------------------------------------------------------------- */
void DumpAtom::write_data(int n, double *buf)
void DumpAtom::write_data(int n, double *mybuf)
{
(this->*write_choice)(n,buf);
(this->*write_choice)(n,mybuf);
}
/* ---------------------------------------------------------------------- */
@ -397,36 +397,36 @@ int DumpAtom::pack_noscale_noimage()
/* ---------------------------------------------------------------------- */
void DumpAtom::write_binary(int n, double *buf)
void DumpAtom::write_binary(int n, double *mybuf)
{
n *= size_one;
fwrite(&n,sizeof(int),1,fp);
fwrite(buf,sizeof(double),n,fp);
fwrite(mybuf,sizeof(double),n,fp);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::write_image(int n, double *buf)
void DumpAtom::write_image(int n, double *mybuf)
{
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
static_cast<int> (buf[m]), static_cast<int> (buf[m+1]),
buf[m+2],buf[m+3],buf[m+4], static_cast<int> (buf[m+5]),
static_cast<int> (buf[m+6]), static_cast<int> (buf[m+7]));
static_cast<int> (mybuf[m]), static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]),
static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7]));
m += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpAtom::write_noimage(int n, double *buf)
void DumpAtom::write_noimage(int n, double *mybuf)
{
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
static_cast<int> (buf[m]), static_cast<int> (buf[m+1]),
buf[m+2],buf[m+3],buf[m+4]);
static_cast<int> (mybuf[m]), static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
m += size_one;
}
}

8
src/dump_cfg.cpp
View File

@ -229,7 +229,7 @@ void DumpCFG::write_header(int n)
write head of block (mass & element name) only if has atoms of the type
------------------------------------------------------------------------- */
void DumpCFG::write_data(int n, double *buf)
void DumpCFG::write_data(int n, double *mybuf)
{
int i,j,m,itype;
int tag_i,index;
@ -241,7 +241,7 @@ void DumpCFG::write_data(int n, double *buf)
if (sort_flag == 0) {
for (i = 0, m = 0; i < n; i++) {
for (j = 0; j < size_one; j++)
rbuf[nlines][j] = buf[m++];
rbuf[nlines][j] = mybuf[m++];
nlines++;
}
@ -282,7 +282,7 @@ void DumpCFG::write_data(int n, double *buf)
// to this index
for (i = 0, m = 0; i < n; i++) {
tag_i = static_cast<int>(buf[m]);
tag_i = static_cast<int>(mybuf[m]);
for (j = 0; j < nchosen; j++) {
if (tag_i == tags[j]) {
index = j;
@ -290,7 +290,7 @@ void DumpCFG::write_data(int n, double *buf)
}
}
for (j = 0; j < size_one; j++)
rbuf[index][j] = buf[m++];
rbuf[index][j] = mybuf[m++];
}
// write data lines in rbuf to file after transfer is done

14
src/dump_custom.cpp
View File

@ -751,31 +751,31 @@ int DumpCustom::pack()
/* ---------------------------------------------------------------------- */
void DumpCustom::write_data(int n, double *buf)
void DumpCustom::write_data(int n, double *mybuf)
{
(this->*write_choice)(n,buf);
(this->*write_choice)(n,mybuf);
}
/* ---------------------------------------------------------------------- */
void DumpCustom::write_binary(int n, double *buf)
void DumpCustom::write_binary(int n, double *mybuf)
{
n *= size_one;
fwrite(&n,sizeof(int),1,fp);
fwrite(buf,sizeof(double),n,fp);
fwrite(mybuf,sizeof(double),n,fp);
}
/* ---------------------------------------------------------------------- */
void DumpCustom::write_text(int n, double *buf)
void DumpCustom::write_text(int n, double *mybuf)
{
int i,j;
int m = 0;
for (i = 0; i < n; i++) {
for (j = 0; j < size_one; j++) {
if (vtype[j] == INT) fprintf(fp,vformat[j],static_cast<int> (buf[m]));
else fprintf(fp,vformat[j],buf[m]);
if (vtype[j] == INT) fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
else fprintf(fp,vformat[j],mybuf[m]);
m++;
}
fprintf(fp,"\n");

10
src/dump_dcd.cpp
View File

@ -233,17 +233,17 @@ int DumpDCD::pack()
/* ---------------------------------------------------------------------- */
void DumpDCD::write_data(int n, double *buf)
void DumpDCD::write_data(int n, double *mybuf)
{
// spread buf atom coords into global arrays
int tag;
int m = 0;
for (int i = 0; i < n; i++) {
tag = static_cast<int> (buf[m]) - 1;
xf[tag] = buf[m+1];
yf[tag] = buf[m+2];
zf[tag] = buf[m+3];
tag = static_cast<int> (mybuf[m]) - 1;
xf[tag] = mybuf[m+1];
yf[tag] = mybuf[m+2];
zf[tag] = mybuf[m+3];
m += size_one;
}

6
src/dump_local.cpp
View File

@ -245,15 +245,15 @@ int DumpLocal::pack()
/* ---------------------------------------------------------------------- */
void DumpLocal::write_data(int n, double *buf)
void DumpLocal::write_data(int n, double *mybuf)
{
int i,j;
int m = 0;
for (i = 0; i < n; i++) {
for (j = 0; j < size_one; j++) {
if (vtype[j] == INT) fprintf(fp,vformat[j],static_cast<int> (buf[m]));
else fprintf(fp,vformat[j],buf[m]);
if (vtype[j] == INT) fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
else fprintf(fp,vformat[j],mybuf[m]);
m++;
}
fprintf(fp,"\n");

14
src/dump_xyz.cpp
View File

@ -155,7 +155,7 @@ int DumpXYZ::pack()
/* ---------------------------------------------------------------------- */
void DumpXYZ::write_data(int n, double *buf)
void DumpXYZ::write_data(int n, double *mybuf)
{
// for group = all, spread buf atom coords into global arrays
// if last chunk of atoms in this snapshot, write global arrays to file
@ -165,12 +165,12 @@ void DumpXYZ::write_data(int n, double *buf)
int m = 0;
for (int i = 0; i < n; i++) {
tag = static_cast<int> (buf[m]) - 1;
types[tag] = static_cast<int> (buf[m+1]);
tag = static_cast<int> (mybuf[m]) - 1;
types[tag] = static_cast<int> (mybuf[m+1]);
j = 3*tag;
coords[j++] = buf[m+2];
coords[j++] = buf[m+3];
coords[j] = buf[m+4];
coords[j++] = mybuf[m+2];
coords[j++] = mybuf[m+3];
coords[j] = mybuf[m+4];
m += size_one;
}
@ -186,7 +186,7 @@ void DumpXYZ::write_data(int n, double *buf)
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
static_cast<int> (buf[m+1]),buf[m+2],buf[m+3],buf[m+4]);
static_cast<int> (mybuf[m+1]),mybuf[m+2],mybuf[m+3],mybuf[m+4]);
m += size_one;
}
}

2
src/style.h
View File

@ -103,6 +103,7 @@ CommandStyle(write_restart,WriteRestart)
#include "compute_erotate_sphere.h"
#include "compute_property_atom.h"
#include "compute_property_local.h"
#include "compute_property_molecule.h"
#include "compute_stress_atom.h"
#include "compute_temp.h"
#include "compute_temp_com.h"
@ -142,6 +143,7 @@ ComputeStyle(reduce/region,ComputeReduceRegion)
ComputeStyle(erotate/sphere,ComputeERotateSphere)
ComputeStyle(property/atom,ComputePropertyAtom)
ComputeStyle(property/local,ComputePropertyLocal)
ComputeStyle(property/molecule,ComputePropertyMolecule)
ComputeStyle(stress/atom,ComputeStressAtom)
ComputeStyle(temp,ComputeTemp)
ComputeStyle(temp/com,ComputeTempCOM)