t_stage *stage;
switch(type) {
+ case STAGE_DISPLACE_ATOM:
+ psize=sizeof(t_displace_atom_params);
+ break;
case STAGE_INSERT_ATOMS:
psize=sizeof(t_insert_atoms_params);
break;
char error[128];
char line[128];
char *wptr;
- char word[16][32];
+ char word[16][64];
int wcnt;
int i,o;
+ t_displace_atom_params dap;
t_insert_atoms_params iap;
t_continue_params cp;
t_anneal_params ap;
wptr=strtok(line," \t");
if(wptr==NULL)
break;
- strncpy(word[wcnt],wptr,32);
+ strncpy(word[wcnt],wptr,64);
wcnt+=1;
}
if(!strncmp(word[1],"lj",2))
mdrun->potential=MOLDYN_POTENTIAL_LJ;
}
+ else if(!strncmp(word[0],"continue",8))
+ strncpy(mdrun->continue_file,word[1],128);
else if(!strncmp(word[0],"cutoff",6))
mdrun->cutoff=atof(word[1]);
else if(!strncmp(word[0],"nnd",3))
mdrun->visualize=atoi(word[1]);
else if(!strncmp(word[0],"stage",5)) {
// for every stage line, add a stage
- if(!strncmp(word[1],"ins_atoms",9)) {
+ if(!strncmp(word[1],"displace",8)) {
+ dap.nr=atoi(word[2]);
+ dap.dx=atof(word[3]);
+ dap.dy=atof(word[4]);
+ dap.dz=atof(word[5]);
+ add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
+ }
+ else if(!strncmp(word[1],"ins_atoms",9)) {
iap.ins_steps=atoi(word[2]);
iap.ins_atoms=atoi(word[3]);
iap.element=atoi(word[4]);
return TRUE;
}
+int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_displace_atom_params *dap;
+ t_stage *stage;
+ t_atom *atom;
+
+ stage=mdrun->stage.current->data;
+ dap=stage->params;
+
+ atom=&(moldyn->atom[dap->nr]);
+ atom->r.x+=dap->dx;
+ atom->r.y+=dap->dy;
+ atom->r.z+=dap->dz;
+
+ return 0;
+}
+
int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
t_insert_atoms_params *iap;
/* stage specific stuff */
switch(stage->type) {
+ case STAGE_DISPLACE_ATOM:
+ stage_print(" -> displace atom\n\n");
+ displace_atom(moldyn,mdrun);
+ change_stage=TRUE;
+ break;
case STAGE_INSERT_ATOMS:
stage_print(" -> insert atoms\n\n");
iap=stage->params;
}
insert_atoms(moldyn,mdrun);
iap->cnt_steps+=1;
- break;
+ break;
case STAGE_CONTINUE:
stage_print(" -> continue\n\n");
if(stage->executed==TRUE) {
}
cp=stage->params;
steps=cp->runs;
- break;
+ break;
case STAGE_ANNEAL:
stage_print(" -> anneal\n\n");
ap=stage->params;
/* sanity check! */
/* prepare simulation */
- moldyn_init(&moldyn,argc,argv);
+
+ if(mdrun.continue_file[0]) {
+ // read the save file
+ moldyn_read_save_file(&moldyn,mdrun.continue_file);
+ // manualaadjusting some stuff
+ moldyn.argc=argc;
+ moldyn.args=argv;
+ rand_init(&(moldyn.random),NULL,1);
+ moldyn.random.status|=RAND_STAT_VERBOSE;
+ }
+ else {
+ moldyn_init(&moldyn,argc,argv);
+ }
+
if(set_int_alg(&moldyn,mdrun.intalgo)<0)
return -1;
+
+ /* potential */
set_cutoff(&moldyn,mdrun.cutoff);
if(set_potential(&moldyn,mdrun.potential)<0)
return -1;
ME,mdrun.potential);
return -1;
}
+
+ /* if it is a continue run, reset schedule and skip lattice init */
+ if(mdrun.continue_file[0]) {
+ memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
+ goto addsched;
+ }
+
+ /* initial lattice and dimensions */
set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
switch(mdrun.lattice) {
return -1;
}
moldyn_bc_check(&moldyn);
+
+ /* temperature and pressure */
set_temperature(&moldyn,mdrun.temperature);
set_pressure(&moldyn,mdrun.pressure);
thermal_init(&moldyn,TRUE);
+
+addsched:
+ /* first schedule */
moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
+
+ /* log */
moldyn_set_log_dir(&moldyn,mdrun.sdir);
moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
if(mdrun.elog)