#include "potentials/harmonic_oscillator.h"
#include "potentials/lennard_jones.h"
#include "potentials/albe.h"
+#include "potentials/albe_orig.h"
#ifdef TERSOFF_ORIG
#include "potentials/tersoff_orig.h"
#else
case STAGE_THERMAL_INIT:
psize=0;
break;
+ case STAGE_CRT:
+ psize=sizeof(t_crt_params);
+ break;
default:
printf("%s unknown stage type: %02x\n",ME,type);
return -1;
t_set_timestep_params stsp;
t_fill_params fp;
t_del_atoms_params delp;
+ t_crt_params crtp;
/* open config file */
fd=open(mdrun->cfile,O_RDONLY);
memset(&stsp,0,sizeof(t_set_timestep_params));
memset(&fp,0,sizeof(t_fill_params));
memset(&delp,0,sizeof(t_del_atoms_params));
+ memset(&crtp,0,sizeof(t_crt_params));
// get command + args
wcnt=0;
if(!strncmp(word[0],"potential",9)) {
if(!strncmp(word[1],"albe",4))
mdrun->potential=MOLDYN_POTENTIAL_AM;
+ if(!strncmp(word[1],"albe_o",6))
+ mdrun->potential=MOLDYN_POTENTIAL_AO;
if(!strncmp(word[1],"tersoff",7))
mdrun->potential=MOLDYN_POTENTIAL_TM;
if(!strncmp(word[1],"ho",2))
case 'e':
cap.type|=CHAATTR_ELEMENT;
break;
+ case 'n':
+ cap.type|=CHAATTR_NUMBER;
default:
break;
}
cap.element=atoi(word[i]);
i+=1;
}
+ if(cap.type&CHAATTR_NUMBER) {
+ cap.element=atoi(word[i]);
+ i+=1;
+ }
for(o=0;o<strlen(word[i]);o++) {
switch(word[i][o]) {
case 'b':
iap.y0=atof(word[9]);
iap.z0=atof(word[10]);
break;
+ case 'P':
+ iap.type=INS_RELPOS;
+ iap.x0=atof(word[8]);
+ iap.y0=atof(word[9]);
+ iap.z0=atof(word[10]);
+ break;
case 'r':
switch(word[8][0]) {
stsp.tau=atof(word[2]);
add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
}
+ else if(!strncmp(word[1],"crt",3)) {
+ crtp.type=atoi(word[2]);
+ crtp.steps=atoi(word[3]);
+ strncpy(crtp.file,word[4],127);
+ add_stage(mdrun,STAGE_CRT,&crtp);
+ }
else {
printf("%s unknown stage type: %s\n",
ME,word[1]);
t_del_atoms_params *delp;
int i;
t_3dvec dist;
-
+ u8 outer;
+
+ outer=0;
stage=mdrun->stage.current->data;
delp=stage->params;
+ if(delp->r<0)
+ outer=1;
+
for(i=0;i<moldyn->count;i++) {
v3_sub(&dist,&(delp->o),&(moldyn->atom[i].r));
//printf("%d ----> %f %f %f = %f | %f\n",i,dist.x,dist.y,dist.z,v3_absolute_square(&dist),delp->r*delp->r);
if(v3_absolute_square(&dist)<=(delp->r*delp->r)) {
- del_atom(moldyn,moldyn->atom[i].tag);
- printf("%s atom deleted: %d %d %d\n",ME,
- moldyn->atom[i].tag,moldyn->atom[i].element,
- moldyn->atom[i].brand);
+ if(!outer) {
+ del_atom(moldyn,moldyn->atom[i].tag);
+ printf("%s atom deleted: %d %d %d\n",ME,
+ moldyn->atom[i].tag,
+ moldyn->atom[i].element,
+ moldyn->atom[i].brand);
+ }
+ }
+ else {
+ if(outer) {
+ del_atom(moldyn,moldyn->atom[i].tag);
+ printf("%s atom deleted: %d %d %d\n",ME,
+ moldyn->atom[i].tag,
+ moldyn->atom[i].element,
+ moldyn->atom[i].brand);
+ }
}
}
cr_check=TRUE;
break;
case INS_POS:
+ case INS_RELPOS:
x0=iap->x0;
y0=iap->y0;
z0=iap->z0;
while(cnt<iap->ins_atoms) {
run=1;
while(run) {
- if(iap->type!=INS_POS) {
+ if((iap->type!=INS_POS)&&(iap->type!=INS_RELPOS)) {
r.x=rand_get_double(&(moldyn->random))*x;
r.y=rand_get_double(&(moldyn->random))*y;
r.z=rand_get_double(&(moldyn->random))*z;
r.y=0.0;
r.z=0.0;
}
- r.x+=x0;
- r.y+=y0;
- r.z+=z0;
+ if(iap->type==INS_RELPOS) {
+ r.x+=x0*mdrun->lc;
+ r.y+=y0*mdrun->lc;
+ r.z+=z0*mdrun->lc;
+ }
+ else {
+ r.x+=x0;
+ r.y+=y0;
+ r.z+=z0;
+ }
// offset
if(iap->type!=INS_TOTAL) {
r.x+=o;
if(cap->element!=atom->element)
continue;
}
+ if(cap->type&CHAATTR_NUMBER) {
+ if(cap->element!=atom->tag)
+ continue;
+ }
if(cap->type&CHAATTR_REGION) {
if(cap->x0>atom->r.x)
continue;
return 0;
}
+int crt(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_stage *stage;
+ t_crt_params *crtp;
+
+ int fd;
+ char line[128];
+ char *wptr;
+ int acount;
+ int ret;
+ void *ptr;
+
+ t_atom *atom;
+ t_3dvec disp;
+ double frac;
+ int i;
+
+ stage=mdrun->stage.current->data;
+ crtp=stage->params;
+
+ acount=0;
+
+ /* initial stuff */
+
+ if(crtp->count==0) {
+ printf(" crt init\n");
+ // read final positions, constraints and do the alloc
+ fd=open(crtp->file,O_RDONLY);
+ if(fd<0) {
+ perror("[mdrun] FATAL reading constraints file");
+ return fd;
+ }
+ while(1) {
+ ret=get_line(fd,line,128);
+ // check for end of file
+ if(ret<=0) {
+ printf(" read %d atom positions\n",acount);
+ if(acount!=moldyn->count)
+ printf(" atom count mismatch!!!\n");
+ printf("\n");
+ break;
+ }
+ // ignore # lines and \n
+ if((line[0]=='#')|(ret==1))
+ continue;
+ // allocate new memory
+ ptr=realloc(crtp->r_fin,(acount+1)*sizeof(t_3dvec));
+ if(ptr==NULL) {
+ perror("[mdrun] FATAL realloc crt positions");
+ return -1;
+ }
+ crtp->r_fin=ptr;
+ ptr=realloc(constraints,(acount+1)*3*sizeof(u8));
+ if(ptr==NULL) {
+ perror("[mdrun] FATAL realloc crt constraints");
+ return -1;
+ }
+ constraints=ptr;
+ // ignore type
+ wptr=strtok(line," \t");
+ // read x y z
+ wptr=strtok(NULL," \t");
+ crtp->r_fin[acount].x=atof(wptr);
+ wptr=strtok(NULL," \t");
+ crtp->r_fin[acount].y=atof(wptr);
+ wptr=strtok(NULL," \t");
+ crtp->r_fin[acount].z=atof(wptr);
+ // read constraints
+ wptr=strtok(NULL," \t");
+ constraints[3*acount]=atoi(wptr);
+ wptr=strtok(NULL," \t");
+ constraints[3*acount+1]=atoi(wptr);
+ wptr=strtok(NULL," \t");
+ constraints[3*acount+2]=atoi(wptr);
+ // done reading
+ acount+=1;
+ }
+ close(fd);
+ // allocate trafo angles
+ trafo_angle=malloc(acount*2*sizeof(double));
+ if(trafo_angle==NULL) {
+ perror("[mdrun] FATAL alloc trafo angles");
+ return -1;
+ }
+ // set crt mode
+ crtt=crtp->type;
+ }
+
+ /* write a save file s-crt_xofy.save */
+ snprintf(line,128,"%s/s-crt_%03dof%03d.save",
+ moldyn->vlsdir,crtp->count,crtp->steps);
+ fd=open(line,O_WRONLY|O_TRUNC|O_CREAT,S_IRUSR|S_IWUSR);
+ if(fd<0) perror("[mdrun] crt save fd open");
+ else {
+ write(fd,moldyn,sizeof(t_moldyn));
+ write(fd,moldyn->atom,
+ moldyn->count*sizeof(t_atom));
+ }
+ close(fd);
+ /* visualize atoms */
+ visual_atoms(moldyn);
+
+ /* output energy */
+ printf(" crt energy: %d - %f\n\n",
+ crtp->count,(moldyn->ekin+moldyn->energy)/EV);
+
+ /* crt routines: calculate displacement + set individual constraints */
+
+ printf(" crt step %d of %d in total\n\n",crtp->count+1,crtp->steps);
+
+ if((crtp->type==1)|(crtp->count==0))
+ printf(" crt angle update\n\n");
+
+ for(i=0;i<moldyn->count;i++) {
+ // calc displacements
+ atom=moldyn->atom;
+ v3_sub(&disp,&(crtp->r_fin[i]),&(atom[i].r));
+ // angles
+ if((crtp->type==1)|(crtp->count==0)) {
+ trafo_angle[2*i]=atan2(disp.x,disp.y);
+ trafo_angle[2*i+1]=-atan2(disp.z,
+ sqrt(disp.x*disp.x+disp.y*disp.y));
+ }
+ // move atoms
+ frac=1.0/(crtp->steps-crtp->count);
+ v3_scale(&disp,&disp,frac);
+ v3_add(&(atom[i].r),&(atom[i].r),&disp);
+ }
+
+ return 0;
+}
+
#define stage_print(m) if(!(stage->executed)) \
printf("%s",m)
t_set_temp_params *stp;
t_set_timestep_params *stsp;
t_fill_params *fp;
+ t_crt_params *crtp;
moldyn=ptr1;
mdrun=ptr2;
thermal_init(moldyn,TRUE);
change_stage=TRUE;
break;
+ case STAGE_CRT:
+ stage_print(" -> constraint relaxation");
+ stage_print(" technique\n\n");
+ crtp=stage->params;
+ if(crtp->count==crtp->steps) {
+ free(constraints);
+ free(trafo_angle);
+ free(crtp->r_fin);
+ change_stage=TRUE;
+ break;
+ }
+ crt(moldyn,mdrun);
+ crtp->count+=1;
+ break;
default:
printf("%s unknwon stage type\n",ME);
break;
memset(&mdrun,0,sizeof(t_mdrun));
memset(&moldyn,0,sizeof(t_moldyn));
+ /* init crt variables */
+ crtt=0;
+ constraints=NULL;
+ trafo_angle=NULL;
+
/* parse arguments */
if(mdrun_parse_argv(&mdrun,argc,argv)<0)
return -1;
mdrun.element1,
mdrun.element2);
break;
+ case MOLDYN_POTENTIAL_AO:
+ albe_orig_mult_set_params(&moldyn,
+ mdrun.element1,
+ mdrun.element2);
+ break;
case MOLDYN_POTENTIAL_TM:
tersoff_mult_set_params(&moldyn,
mdrun.element1,
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