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Fix code for AVX and remove warnings

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2022-11-08 15:30:37 +01:00
parent 437b380229
commit 493915fe95
10 changed files with 51 additions and 36 deletions
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30
lammps/atom.c
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@@ -4,8 +4,8 @@
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
*/
#include <stdlib.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
@@ -186,7 +186,7 @@ int readAtom_pdb(Atom* atom, Parameter* param) {
}
while(!feof(fp)) {
fgets(line, MAXLINE, fp);
readline(line, fp);
char *item = strtok(line, " ");
if(strncmp(item, "CRYST1", 6) == 0) {
param->xlo = 0.0;
@@ -273,15 +273,15 @@ int readAtom_gro(Atom* atom, Parameter* param) {
return -1;
}
fgets(desc, MAXLINE, fp);
readline(desc, fp);
for(i = 0; desc[i] != '\n'; i++);
desc[i] = '\0';
fgets(line, MAXLINE, fp);
readline(line, fp);
atoms_to_read = atoi(strtok(line, " "));
fprintf(stdout, "System: %s with %d atoms\n", desc, atoms_to_read);
while(!feof(fp) && read_atoms < atoms_to_read) {
fgets(line, MAXLINE, fp);
readline(line, fp);
char *label = strtok(line, " ");
int type = type_str2int(strtok(NULL, " "));
int atom_id = atoi(strtok(NULL, " ")) - 1;
@@ -304,7 +304,7 @@ int readAtom_gro(Atom* atom, Parameter* param) {
}
if(!feof(fp)) {
fgets(line, MAXLINE, fp);
readline(line, fp);
param->xlo = 0.0;
param->xhi = atof(strtok(line, " "));
param->ylo = 0.0;
@@ -353,15 +353,15 @@ int readAtom_dmp(Atom* atom, Parameter* param) {
}
while(!feof(fp) && ts < 1 && !read_atoms) {
fgets(line, MAXLINE, fp);
readline(line, fp);
if(strncmp(line, "ITEM: ", 6) == 0) {
char *item = &line[6];
if(strncmp(item, "TIMESTEP", 8) == 0) {
fgets(line, MAXLINE, fp);
readline(line, fp);
ts = atoi(line);
} else if(strncmp(item, "NUMBER OF ATOMS", 15) == 0) {
fgets(line, MAXLINE, fp);
readline(line, fp);
natoms = atoi(line);
atom->Natoms = natoms;
atom->Nlocal = natoms;
@@ -369,23 +369,23 @@ int readAtom_dmp(Atom* atom, Parameter* param) {
growAtom(atom);
}
} else if(strncmp(item, "BOX BOUNDS pp pp pp", 19) == 0) {
fgets(line, MAXLINE, fp);
readline(line, fp);
param->xlo = atof(strtok(line, " "));
param->xhi = atof(strtok(NULL, " "));
param->xprd = param->xhi - param->xlo;
fgets(line, MAXLINE, fp);
readline(line, fp);
param->ylo = atof(strtok(line, " "));
param->yhi = atof(strtok(NULL, " "));
param->yprd = param->yhi - param->ylo;
fgets(line, MAXLINE, fp);
readline(line, fp);
param->zlo = atof(strtok(line, " "));
param->zhi = atof(strtok(NULL, " "));
param->zprd = param->zhi - param->zlo;
} else if(strncmp(item, "ATOMS id type x y z vx vy vz", 28) == 0) {
for(int i = 0; i < natoms; i++) {
fgets(line, MAXLINE, fp);
readline(line, fp);
atom_id = atoi(strtok(line, " ")) - 1;
atom->type[atom_id] = atoi(strtok(NULL, " "));
atom_x(atom_id) = atof(strtok(NULL, " "));
@@ -442,7 +442,7 @@ int readAtom_in(Atom* atom, Parameter* param) {
return -1;
}
fgets(line, MAXLINE, fp);
readline(line, fp);
natoms = atoi(strtok(line, " "));
param->xlo = atof(strtok(NULL, " "));
param->xhi = atof(strtok(NULL, " "));
@@ -459,7 +459,7 @@ int readAtom_in(Atom* atom, Parameter* param) {
}
for(int i = 0; i < natoms; i++) {
fgets(line, MAXLINE, fp);
readline(line, fp);
// TODO: store mass per atom
char *s_mass = strtok(line, " ");