void wjzmat(char *filename, int atomnum, ATOM atom[], MOLINFO minfo)
{
FILE *fpout;
int i;
/* int index; */
char tmpchar0[10];
char tmpchar1[10];
char tmpchar2[10];
char tmpchar3[10];
if ((fpout = fopen(filename, "w")) == NULL) {
fprintf(stderr, "Cannot open file %s, exit\n", filename);
exit(1);
}
intercoord(atomnum, atom);
fprintf(fpout, "%s\n", "This Jaguar input file generated by Antechamber");
fprintf(fpout, "%s\n", "&gen");
fprintf(fpout, "%s%d\n", "molchg=", minfo.icharge);
fprintf(fpout, "%s%d\n", "multip=", minfo.multiplicity);
fprintf(fpout, "igeopt=1\n");
fprintf(fpout, "basis=6-31G*\n");
fprintf(fpout, "dft=b3lyp\n");
fprintf(fpout, "%s\n", "&");
fprintf(fpout, "%s\n", "&zmat");
for (i = 0; i < atomnum; i++) {
newitoa(i + 1, tmpchar0);
if (i == 0) {
fprintf(fpout, "%8s\n", atom[i].name);
continue;
}
if (i == 1) {
strcpy(tmpchar1, "r");
strcat(tmpchar1, tmpchar0);
fprintf(fpout, "%8s%8s%8s\n", atom[i].name,
atom[atom[i].bondatom].name, tmpchar1);
continue;
}
if (i == 2) {
strcpy(tmpchar1, "r");
strcat(tmpchar1, tmpchar0);
fprintf(fpout, "%8s%8s%8s", atom[i].name,
atom[atom[i].bondatom].name , tmpchar1);
strcpy(tmpchar2, "a");
strcat(tmpchar2, tmpchar0);
fprintf(fpout, "%8s%8s\n", atom[atom[i].angleatom].name , tmpchar2);
continue;
}
strcpy(tmpchar1, "r");
strcat(tmpchar1, tmpchar0);
fprintf(fpout, "%8s%8s%8s", atom[i].name, atom[atom[i].bondatom].name ,
tmpchar1);
strcpy(tmpchar2, "a");
strcat(tmpchar2, tmpchar0);
fprintf(fpout, "%8s%8s", atom[atom[i].angleatom].name , tmpchar2);
strcpy(tmpchar3, "d");
strcat(tmpchar3, tmpchar0);
fprintf(fpout, "%8s%8s\n", atom[atom[i].twistatom].name, tmpchar3);
}
fprintf(fpout, "&\n&zvar\n");
fprintf(fpout, "r2= %13.8lf\n", atom[1].bond);
fprintf(fpout, "r3= %13.8lf ", atom[2].bond);
fprintf(fpout, "a3= %13.8lf\n", atom[2].angle);
for (i = 3; i < atomnum; i++) {
newitoa(i + 1, tmpchar0);
strcpy(tmpchar1, "r");
strcat(tmpchar1, tmpchar0);
strcpy(tmpchar2, "a");
strcat(tmpchar2, tmpchar0);
strcpy(tmpchar3, "d");
strcat(tmpchar3, tmpchar0);
fprintf(fpout, "%s= %13.8lf ", tmpchar1, atom[i].bond);
fprintf(fpout, "%s= %13.8lf ", tmpchar2, atom[i].angle);
fprintf(fpout, "%s= %13.8lf\n", tmpchar3, atom[i].twist);
}
fprintf(fpout, "&\n\n");
fclose(fpout);
}
void wgzmat(char *filename, int atomnum, ATOM atom[], MOLINFO minfo)
{
FILE *fpout;
int i;
/* int index; */
char tmpchar0[10];
char tmpchar1[10];
char tmpchar2[10];
char tmpchar3[10];
if ((fpout = fopen(filename, "w")) == NULL) {
fprintf(stderr, "Cannot open file %s, exit\n", filename);
exit(1);
}
intercoord(atomnum, atom);
fprintf(fpout, "%s\n", "--Link1--");
fprintf(fpout, "%s%s\n", "%chk=", minfo.chkfile);
fprintf(fpout, "%s\n\n", minfo.gkeyword);
fprintf(fpout, "%s\n\n", "remark line goes here");
fprintf(fpout, "%d%4d\n", minfo.icharge, minfo.multiplicity);
element(atomnum, atom);
for (i = 0; i < atomnum; i++) {
newitoa(i + 1, tmpchar0);
if (i == 0) {
fprintf(fpout, "%5s\n", atom[i].element);
continue;
}
if (i == 1) {
strcpy(tmpchar1, "b");
strcat(tmpchar1, tmpchar0);
fprintf(fpout, "%5s%5d%8s\n", atom[i].element,
atom[i].bondatom + 1, tmpchar1);
continue;
}
if (i == 2) {
strcpy(tmpchar1, "b");
strcat(tmpchar1, tmpchar0);
fprintf(fpout, "%5s%5d%8s", atom[i].element,
atom[i].bondatom + 1, tmpchar1);
strcpy(tmpchar2, "a");
strcat(tmpchar2, tmpchar0);
fprintf(fpout, "%5d%8s\n", atom[i].angleatom + 1, tmpchar2);
continue;
}
strcpy(tmpchar1, "b");
strcat(tmpchar1, tmpchar0);
fprintf(fpout, "%5s%5d%8s", atom[i].element, atom[i].bondatom + 1,
tmpchar1);
strcpy(tmpchar2, "a");
strcat(tmpchar2, tmpchar0);
fprintf(fpout, "%5d%8s", atom[i].angleatom + 1, tmpchar2);
strcpy(tmpchar3, "t");
strcat(tmpchar3, tmpchar0);
fprintf(fpout, "%5d%8s\n", atom[i].twistatom + 1, tmpchar3);
}
fprintf(fpout, "Variables:\n");
fprintf(fpout, "b2= %8.4lf\n", atom[1].bond);
fprintf(fpout, "b3= %8.4lf\n", atom[2].bond);
fprintf(fpout, "a3= %8.4lf\n", atom[2].angle);
for (i = 3; i < atomnum; i++) {
newitoa(i + 1, tmpchar0);
strcpy(tmpchar1, "b");
strcat(tmpchar1, tmpchar0);
strcpy(tmpchar2, "a");
strcat(tmpchar2, tmpchar0);
strcpy(tmpchar3, "t");
strcat(tmpchar3, tmpchar0);
fprintf(fpout, "%s= %8.4lf\n", tmpchar1, atom[i].bond);
fprintf(fpout, "%s= %8.4lf\n", tmpchar2, atom[i].angle);
fprintf(fpout, "%s= %8.4lf\n", tmpchar3, atom[i].twist);
}
fprintf(fpout, "\n");
fclose(fpout);
}
void wgzmat(char *filename, int atomnum, ATOM atom[], MOLINFO minfo)
{
FILE *fpin;
FILE *fpout;
char *amberhome;
char espparm_file[MAXCHAR];
char line[MAXCHAR];
char akeyword[MAXCHAR]="";
char ckeyword[MAXCHAR];
char tmpchar0[MAXCHAR];
char tmpchar1[MAXCHAR];
char tmpchar2[MAXCHAR];
char tmpchar3[MAXCHAR];
int i,j;
int iradius_flag;
int ibs= 0;
int esp_flag;
int nespparm = 0;
int nbasisset = 0;
double default_radius = 1.7;
ESPPARM espparm[120];
BASISSET basisset[100];
if ((fpout = fopen(filename, "w")) == NULL) {
fprintf(stdout, "Cannot open a file %s to write in wgzmat(), exit\n", filename);
exit(1);
}
intercoord(atomnum, atom);
fprintf(fpout, "%s\n", "--Link1--");
if(strlen(minfo.gn) >= 5)
fprintf(fpout, "%s\n", minfo.gn);
fprintf(fpout, "%s%s\n", "%chk=", minfo.chkfile);
if(strlen(minfo.gm) >= 4)
fprintf(fpout, "%s\n", minfo.gm);
// check ESP-related keyword
esp_flag = 0;
for(i=0;i<strlen(minfo.gkeyword);i++)
ckeyword[i] = toupper(minfo.gkeyword[i]);
if((strstr(ckeyword, "POP=") != 0 || strstr(ckeyword, "POP(") != 0) &&
(strstr(ckeyword, "MK") != 0 || strstr(ckeyword, "CHELP") != 0))
esp_flag = 1;
// when the default gaussian keyword is used, or esp_flag ==1, read ESP.PARM
if(minfo.igkeyword == 0 || esp_flag == 1) {
amberhome = (char *) getenv("AMBERHOME");
if( amberhome == NULL ){
fprintf( stdout, "AMBERHOME is not set!\n" );
exit(1);
}
strcpy(espparm_file, amberhome);
strcat(espparm_file, "/dat/antechamber/ESPPARM.DAT");
if ((fpin = fopen(espparm_file, "r")) == NULL) {
fprintf(stdout, "Cannot open espparm_file %s in read_espparm(), exit\n", espparm_file);
exit(1);
}
for (;;) {
if (fgets(line, MAXCHAR, fpin) == NULL) break;
if(strncmp(line, "DEFAULT RADIUS", 14) == 0)
sscanf(&line[14], "%lf", &default_radius);
if(strncmp(line, "BASIS SET", 9) == 0) {
sscanf(&line[9], "%d%s", &basisset[nbasisset].id,
basisset[nbasisset].bs);
nbasisset++;
}
if(strncmp(line, "PARM", 4) == 0) {
sscanf(&line[4], "%d%s%lf%lf%d%d", &espparm[nespparm].atomicnum, espparm[nespparm].elem,
&espparm[nespparm].vdw, &espparm[nespparm].mk,
&espparm[nespparm].flag, &espparm[nespparm].bs);
nespparm++;
}
}
fclose(fpin);
iradius_flag = 0;
ibs = 0;
for(i=0;i<atomnum;i++) {
for(j=0;j<nespparm;j++)
if(atom[i].atomicnum == espparm[j].atomicnum || strcmp(atom[i].element, espparm[j].elem) == 0) {
if(ibs < espparm[j].bs) ibs=espparm[j].bs;
if(espparm[j].flag != 0) {
iradius_flag = 1;
espparm[j].flag = 2;
}
break;
}
}
if(minfo.igkeyword == 0) {
strcpy(minfo.gkeyword, "#HF/");
strcat(minfo.gkeyword, basisset[ibs-1].bs);
strcat(minfo.gkeyword, " SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt");
}
}
// additional keywords
if(esp_flag == 1) {
if(iradius_flag == 1) {
if(strstr(minfo.gkeyword, "ReadRadii") == 0 &&
strstr(minfo.gkeyword, "READRADII") == 0 &&
strstr(minfo.gkeyword, "readradii") == 0) {
strcat(akeyword, "Pop=ReadRadii");
}
}
if(minfo.gv == 1) {
if(strstr(minfo.gkeyword, "6/50=1") == 0) {
strcat(akeyword, " iop(6/50=1)");
}
}
}
if(strlen(akeyword) >= 1) {
fprintf(fpout, "%s\n", minfo.gkeyword);
fprintf(fpout, "#%s\n", akeyword);
fprintf(fpout, "\n");
}
else
fprintf(fpout, "%s\n\n", minfo.gkeyword);
fprintf(fpout, "%s\n\n", "remark line goes here");
fprintf(fpout, "%d%4d\n", minfo.icharge, minfo.multiplicity);
element(atomnum, atom);
for (i = 0; i < atomnum; i++) {
/* newitoa(i + 1, tmpchar0); */
sprintf(tmpchar0, "%d", i+1);
if (i == 0) {
fprintf(fpout, "%5s\n", atom[i].element);
continue;
}
if (i == 1) {
strcpy(tmpchar1, "b");
strcat(tmpchar1, tmpchar0);
fprintf(fpout, "%5s%5d%8s\n", atom[i].element,
atom[i].bondatom + 1, tmpchar1);
continue;
}
if (i == 2) {
strcpy(tmpchar1, "b");
strcat(tmpchar1, tmpchar0);
fprintf(fpout, "%5s%5d%8s", atom[i].element,
atom[i].bondatom + 1, tmpchar1);
strcpy(tmpchar2, "a");
strcat(tmpchar2, tmpchar0);
fprintf(fpout, "%5d%8s\n", atom[i].angleatom + 1, tmpchar2);
continue;
}
strcpy(tmpchar1, "b");
strcat(tmpchar1, tmpchar0);
fprintf(fpout, "%5s%5d%8s", atom[i].element, atom[i].bondatom + 1,
tmpchar1);
strcpy(tmpchar2, "a");
strcat(tmpchar2, tmpchar0);
fprintf(fpout, "%5d%8s", atom[i].angleatom + 1, tmpchar2);
strcpy(tmpchar3, "t");
strcat(tmpchar3, tmpchar0);
fprintf(fpout, "%5d%8s\n", atom[i].twistatom + 1, tmpchar3);
}
fprintf(fpout, "Variables:\n");
fprintf(fpout, "b2= %8.4lf\n", atom[1].bond);
fprintf(fpout, "b3= %8.4lf\n", atom[2].bond);
fprintf(fpout, "a3= %8.4lf\n", atom[2].angle);
for (i = 3; i < atomnum; i++) {
/* newitoa(i + 1, tmpchar0); */
sprintf(tmpchar0, "%d", i+1);
strcpy(tmpchar1, "b");
strcat(tmpchar1, tmpchar0);
strcpy(tmpchar2, "a");
strcat(tmpchar2, tmpchar0);
strcpy(tmpchar3, "t");
strcat(tmpchar3, tmpchar0);
fprintf(fpout, "%s= %8.4lf\n", tmpchar1, atom[i].bond);
fprintf(fpout, "%s= %8.4lf\n", tmpchar2, atom[i].angle);
fprintf(fpout, "%s= %8.4lf\n", tmpchar3, atom[i].twist);
}
if(esp_flag == 1) {
if(minfo.gv == 1 && iradius_flag == 1) {
for(i=0;i<nespparm;i++)
if(espparm[i].flag == 2) {
if(espparm[i].mk <= 0) espparm[i].mk=default_radius;
fprintf(fpout, "\n%s %8.2lf", espparm[i].elem, espparm[i].mk);
}
fprintf(fpout, "\n\n%s\n", minfo.gesp);
for(i=0;i<nespparm;i++)
if(espparm[i].flag == 2) {
if(espparm[i].mk <= 0) espparm[i].mk=default_radius;
fprintf(fpout, "\n%s %8.2lf", espparm[i].elem, espparm[i].mk);
}
fprintf(fpout, "\n\n%s\n", minfo.gesp);
}
if(minfo.gv == 0 && iradius_flag == 1) {
for(i=0;i<nespparm;i++)
if(espparm[i].flag == 2) {
if(espparm[i].mk <= 0) espparm[i].mk=default_radius;
fprintf(fpout, "\n%s %8.2lf", espparm[i].elem, espparm[i].mk);
}
fprintf(fpout, "\n");
for(i=0;i<nespparm;i++)
if(espparm[i].flag == 2) {
if(espparm[i].mk <= 0) espparm[i].mk=default_radius;
fprintf(fpout, "\n%s %8.2lf", espparm[i].elem, espparm[i].mk);
}
fprintf(fpout, "\n");
}
if(minfo.gv == 1 && iradius_flag == 0) {
fprintf(fpout, "\n%s\n", minfo.gesp);
fprintf(fpout, "\n%s\n", minfo.gesp);
}
}
fprintf(fpout, "\n\n");
fclose(fpout);
}
