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Ncmexp2717/md2axsf.c Secret

Created October 1, 2020 17:17
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For MD files in molecular dynamics
Raw
md2axsf.c
/**********************************************************************
md2axsf.c:
md2axsf.c is a routine to convert a md file to a axsf file.
This code follows GNU-GPL.
Compile: gcc md2axsf.c -lm -o md2axsf
usage: ./md2axsf input.md output.axsf
Log of md2axsf.c:
March/15/2016 Released by T. Ozaki
October/02/2020 Modified by N. Yamaguchi
***********************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#define strsize 600
char Atom_Symbol[105][4];
void Set_Atom_Symbol();
int Atomic_Number(char species[4]);
int main(int argc, char *argv[])
{
int i,j,k,ns,na;
int nline,atomnum,numsnapshot;
FILE *fp1,*fp0;
char read_str[strsize];
double tv[4][4],tmp,x,y,z;
Set_Atom_Symbol();
/* count the number of lines */
if ((fp1 = fopen(argv[1],"r")) != NULL){
nline = 0;
while (fgets(read_str, strsize, fp1)!=NULL){
nline++;
}
fclose(fp1);
}
else{
printf("could not find %s\n",argv[1]);
}
/* read the number of atoms */
if ((fp1 = fopen(argv[1],"r")) != NULL){
fscanf(fp1,"%ld",&atomnum);
fclose(fp1);
}
else{
printf("could not find %s\n",argv[1]);
}
numsnapshot = nline/(atomnum+2);
/* read the file again, and save the corresponding axsf file */
if ((fp0 = fopen(argv[2],"w")) != NULL){
fprintf(fp0,"ANIMSTEPS %d\n",numsnapshot);
fprintf(fp0,"CRYSTAL\n");
if ((fp1 = fopen(argv[1],"r")) != NULL){
for (ns=1; ns<=numsnapshot; ns++){
/* Added by N. Yamaguchi ***/
#if 0
/* ***/
fscanf(fp1,"%s",read_str); /* atomnum */
fscanf(fp1,"%s",read_str); /* time= */
fscanf(fp1,"%s",read_str); /* 0.0000 */
fscanf(fp1,"%s",read_str); /* (fs) */
fscanf(fp1,"%s",read_str); /* Energy= */
fscanf(fp1,"%s",read_str); /* -8.20219 */
fscanf(fp1,"%s",read_str); /* (Hartree) */
fscanf(fp1,"%s",read_str); /* Cell_Vectors= */
/* Added by N. Yamaguchi ***/
#else
do {
fscanf(fp1,"%s",read_str);
} while (strcmp(read_str, "Cell_Vectors="));
#endif
/* ***/
fscanf(fp1,"%lf",&tv[1][1]);
fscanf(fp1,"%lf",&tv[1][2]);
fscanf(fp1,"%lf",&tv[1][3]);
fscanf(fp1,"%lf",&tv[2][1]);
fscanf(fp1,"%lf",&tv[2][2]);
fscanf(fp1,"%lf",&tv[2][3]);
fscanf(fp1,"%lf",&tv[3][1]);
fscanf(fp1,"%lf",&tv[3][2]);
fscanf(fp1,"%lf",&tv[3][3]);
fprintf(fp0,"PRIMVEC %d\n",ns);
for (i=1; i<=3; i++){
for (j=1; j<=3; j++){
fprintf(fp0," %15.7f ",tv[i][j]);
}
fprintf(fp0,"\n");
}
fprintf(fp0,"PRIMCOORD %d\n",ns);
fprintf(fp0," %d %d\n",atomnum,1);
for (na=1; na<=atomnum; na++){
fscanf(fp1,"%s",read_str);
fscanf(fp1,"%lf",&x);
fscanf(fp1,"%lf",&y);
fscanf(fp1,"%lf",&z);
fscanf(fp1,"%lf",&tmp);
fscanf(fp1,"%lf",&tmp);
fscanf(fp1,"%lf",&tmp);
fscanf(fp1,"%lf",&tmp);
fscanf(fp1,"%lf",&tmp);
fscanf(fp1,"%lf",&tmp);
fscanf(fp1,"%lf",&tmp);
fscanf(fp1,"%lf",&tmp);
fscanf(fp1,"%lf",&tmp);
fscanf(fp1,"%lf",&tmp);
fprintf(fp0," %3d ",Atomic_Number(read_str));
fprintf(fp0,"%15.7f",x);
fprintf(fp0,"%15.7f",y);
fprintf(fp0,"%15.7f\n",z);
}
}
fclose(fp1);
}
else{
printf("could not find %s\n",argv[1]);
}
fclose(fp0);
}
else{
printf("could not find %s\n",argv[2]);
}
}
int Atomic_Number(char species[4])
{
int i,po;
i = 0;
po = 0;
do {
if (strncmp(species,Atom_Symbol[i],4)==0)
po = 1;
else
i++;
} while (po==0 && i<104);
return i;
}
void Set_Atom_Symbol()
{
strcpy(Atom_Symbol[ 0], "E");
strcpy(Atom_Symbol[ 1], "H");
strcpy(Atom_Symbol[ 2], "He");
strcpy(Atom_Symbol[ 3], "Li");
strcpy(Atom_Symbol[ 4], "Be");
strcpy(Atom_Symbol[ 5], "B");
strcpy(Atom_Symbol[ 6], "C");
strcpy(Atom_Symbol[ 7], "N");
strcpy(Atom_Symbol[ 8], "O");
strcpy(Atom_Symbol[ 9], "F");
strcpy(Atom_Symbol[ 10], "Ne");
strcpy(Atom_Symbol[ 11], "Na");
strcpy(Atom_Symbol[ 12], "Mg");
strcpy(Atom_Symbol[ 13], "Al");
strcpy(Atom_Symbol[ 14], "Si");
strcpy(Atom_Symbol[ 15], "P");
strcpy(Atom_Symbol[ 16], "S");
strcpy(Atom_Symbol[ 17], "Cl");
strcpy(Atom_Symbol[ 18], "Ar");
strcpy(Atom_Symbol[ 19], "K");
strcpy(Atom_Symbol[ 20], "Ca");
strcpy(Atom_Symbol[ 21], "Sc");
strcpy(Atom_Symbol[ 22], "Ti");
strcpy(Atom_Symbol[ 23], "V");
strcpy(Atom_Symbol[ 24], "Cr");
strcpy(Atom_Symbol[ 25], "Mn");
strcpy(Atom_Symbol[ 26], "Fe");
strcpy(Atom_Symbol[ 27], "Co");
strcpy(Atom_Symbol[ 28], "Ni");
strcpy(Atom_Symbol[ 29], "Cu");
strcpy(Atom_Symbol[ 30], "Zn");
strcpy(Atom_Symbol[ 31], "Ga");
strcpy(Atom_Symbol[ 32], "Ge");
strcpy(Atom_Symbol[ 33], "As");
strcpy(Atom_Symbol[ 34], "Se");
strcpy(Atom_Symbol[ 35], "Br");
strcpy(Atom_Symbol[ 36], "Kr");
strcpy(Atom_Symbol[ 37], "Rb");
strcpy(Atom_Symbol[ 38], "Sr");
strcpy(Atom_Symbol[ 39], "Y");
strcpy(Atom_Symbol[ 40], "Zr");
strcpy(Atom_Symbol[ 41], "Nb");
strcpy(Atom_Symbol[ 42], "Mo");
strcpy(Atom_Symbol[ 43], "Tc");
strcpy(Atom_Symbol[ 44], "Ru");
strcpy(Atom_Symbol[ 45], "Rh");
strcpy(Atom_Symbol[ 46], "Pd");
strcpy(Atom_Symbol[ 47], "Ag");
strcpy(Atom_Symbol[ 48], "Cd");
strcpy(Atom_Symbol[ 49], "In");
strcpy(Atom_Symbol[ 50], "Sn");
strcpy(Atom_Symbol[ 51], "Sb");
strcpy(Atom_Symbol[ 52], "Te");
strcpy(Atom_Symbol[ 53], "I");
strcpy(Atom_Symbol[ 54], "Xe");
strcpy(Atom_Symbol[ 55], "Cs");
strcpy(Atom_Symbol[ 56], "Ba");
strcpy(Atom_Symbol[ 57], "La");
strcpy(Atom_Symbol[ 58], "Ce");
strcpy(Atom_Symbol[ 59], "Pr");
strcpy(Atom_Symbol[ 60], "Nd");
strcpy(Atom_Symbol[ 61], "Pm");
strcpy(Atom_Symbol[ 62], "Sm");
strcpy(Atom_Symbol[ 63], "Eu");
strcpy(Atom_Symbol[ 64], "Gd");
strcpy(Atom_Symbol[ 65], "Tb");
strcpy(Atom_Symbol[ 66], "Dy");
strcpy(Atom_Symbol[ 67], "Ho");
strcpy(Atom_Symbol[ 68], "Er");
strcpy(Atom_Symbol[ 69], "Tm");
strcpy(Atom_Symbol[ 70], "Yb");
strcpy(Atom_Symbol[ 71], "Lu");
strcpy(Atom_Symbol[ 72], "Hf");
strcpy(Atom_Symbol[ 73], "Ta");
strcpy(Atom_Symbol[ 74], "W");
strcpy(Atom_Symbol[ 75], "Re");
strcpy(Atom_Symbol[ 76], "Os");
strcpy(Atom_Symbol[ 77], "Ir");
strcpy(Atom_Symbol[ 78], "Pt");
strcpy(Atom_Symbol[ 79], "Au");
strcpy(Atom_Symbol[ 80], "Hg");
strcpy(Atom_Symbol[ 81], "Tl");
strcpy(Atom_Symbol[ 82], "Pb");
strcpy(Atom_Symbol[ 83], "Bi");
strcpy(Atom_Symbol[ 84], "Po");
strcpy(Atom_Symbol[ 85], "At");
strcpy(Atom_Symbol[ 86], "Rn");
strcpy(Atom_Symbol[ 87], "Fr");
strcpy(Atom_Symbol[ 88], "Ra");
strcpy(Atom_Symbol[ 89], "Ac");
strcpy(Atom_Symbol[ 90], "Th");
strcpy(Atom_Symbol[ 91], "Pa");
strcpy(Atom_Symbol[ 92], "U");
strcpy(Atom_Symbol[ 93], "Np");
strcpy(Atom_Symbol[ 94], "Pu");
strcpy(Atom_Symbol[ 95], "Am");
strcpy(Atom_Symbol[ 96], "Cm");
strcpy(Atom_Symbol[ 97], "Bk");
strcpy(Atom_Symbol[ 98], "Cf");
strcpy(Atom_Symbol[ 99], "Es");
strcpy(Atom_Symbol[100], "Fm");
strcpy(Atom_Symbol[101], "Md");
strcpy(Atom_Symbol[102], "No");
strcpy(Atom_Symbol[103], "Lr");
}
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