added partition support in create_lattice function

[physik/posic.git] / mdrun.c

diff --git a/mdrun.c b/mdrun.c
index af8a352..83f501c 100644 (file)
--- a/mdrun.c
+++ b/mdrun.c
@@ -17,6 +17,11 @@
 #include "potentials/tersoff.h"
 #endif
 
+/* pse */
+#define PSE_MASS
+#include "pse.h"
+#undef PSE_MASS
+
 #define ME     "[mdrun]"
 
 /*
@@ -111,6 +116,12 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
                case STAGE_CHSATTR:
                        psize=sizeof(t_chsattr_params);
                        break;
+               case STAGE_SET_TEMP:
+                       psize=sizeof(t_set_temp_params);
+                       break;
+               case STAGE_SET_TIMESTEP:
+                       psize=sizeof(t_set_timestep_params);
+                       break;
                default:
                        printf("%s unknown stage type: %02x\n",ME,type);
                        return -1;
@@ -155,6 +166,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
        t_anneal_params ap;
        t_chaattr_params cap;
        t_chsattr_params csp;
+       t_set_temp_params stp;
+       t_set_timestep_params stsp;
 
        /* open config file */
        fd=open(mdrun->cfile,O_RDONLY);
@@ -184,6 +197,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                memset(&ap,0,sizeof(t_anneal_params));
                memset(&cap,0,sizeof(t_chaattr_params));
                memset(&csp,0,sizeof(t_chsattr_params));
+               memset(&stp,0,sizeof(t_set_temp_params));
+               memset(&stsp,0,sizeof(t_set_timestep_params));
 
                // get command + args
                wcnt=0;
@@ -269,6 +284,14 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                        mdrun->ly=atoi(word[3]);
                        mdrun->lz=atoi(word[4]);
                        mdrun->lc=atof(word[5]);
+                       if(wcnt==8) {
+                               mdrun->fill_element=atoi(word[6]);
+                               mdrun->fill_brand=atoi(word[7]);
+                       }
+                       else {
+                               mdrun->fill_element=mdrun->element1;
+                               mdrun->fill_brand=0;
+                       }
                }
                else if(!strncmp(word[0],"aattr",5)) {
                        // for aatrib line we need a special stage
@@ -507,8 +530,24 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                                ap.count=0;
                                ap.runs=atoi(word[2]);
                                ap.dt=atof(word[3]);
+                               ap.interval=atoi(word[4]);
                                add_stage(mdrun,STAGE_ANNEAL,&ap);
                        }
+                       else if(!strncmp(word[1],"set_temp",8)) {
+                               if(word[2][0]=='c') {
+                                       stp.type=SET_TEMP_CURRENT;
+                                       stp.val=0.0;
+                               }
+                               else {
+                                       stp.type=SET_TEMP_VALUE;
+                                       stp.val=atof(word[2]);
+                               }
+                               add_stage(mdrun,STAGE_SET_TEMP,&stp);
+                       }
+                       else if(!strncmp(word[1],"set_timestep",12)) {
+                               stsp.tau=atof(word[2]);
+                               add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
+                       }
                        else {
                                printf("%s unknown stage type: %s\n",
                                       ME,word[1]);
@@ -836,7 +875,6 @@ int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
                }
                atom->attr=cap->attr;
        }
-       printf("     atom attributes: %02x\n\n",cap->attr);
 
        return 0;
 }
@@ -898,13 +936,14 @@ int mdrun_hook(void *ptr1,void *ptr2) {
        t_stage *stage;
        t_list *sl;
        int steps;
-       double tau;
        u8 change_stage;
 
        t_insert_atoms_params *iap;
        t_insert_mixed_atoms_params *imp;
        t_continue_params *cp;
        t_anneal_params *ap;
+       t_set_temp_params *stp;
+       t_set_timestep_params *stsp;
 
        moldyn=ptr1;
        mdrun=ptr2;
@@ -920,9 +959,8 @@ int mdrun_hook(void *ptr1,void *ptr2) {
        /* get stage description */
        stage=sl->current->data;
 
-       /* default steps and tau values */
+       /* steps in next schedule */
        steps=mdrun->relax_steps;
-       tau=mdrun->timestep;
 
        /* check whether relaxation steps are necessary */
        if((check_pressure(moldyn,mdrun)==TRUE)&\
@@ -982,17 +1020,35 @@ int mdrun_hook(void *ptr1,void *ptr2) {
                                        set_temperature(moldyn,
                                                        moldyn->t_ref+ap->dt);
                                ap->count+=1;
+                               steps=ap->interval;
                                break;
                        case STAGE_CHAATTR:
-                               stage_print("  -> chaattr\n\n");
+                               stage_print("  -> change atom attributes\n\n");
                                chaatr(moldyn,mdrun);
                                change_stage=TRUE;
                                break;
                        case STAGE_CHSATTR:
-                               stage_print("  -> chsattr\n\n");
+                               stage_print("  -> change sys attributes\n\n");
                                chsattr(moldyn,mdrun);
                                change_stage=TRUE;
                                break;
+                       case STAGE_SET_TEMP:
+                               stage_print("  -> set temperature\n\n");
+                               stp=stage->params;
+                               if(stp->type&SET_TEMP_CURRENT) {
+                                       set_temperature(moldyn,moldyn->t_avg);
+                               }
+                               else {
+                                       set_temperature(moldyn,stp->val);
+                               }
+                               change_stage=TRUE;
+                               break;
+                       case STAGE_SET_TIMESTEP:
+                               stage_print("  -> set timestep\n\n");
+                               stsp=stage->params;
+                               mdrun->timestep=stsp->tau;
+                               change_stage=TRUE;
+                               break;
                        default:
                                printf("%s unknwon stage type\n",ME);
                                break;
@@ -1009,7 +1065,6 @@ int mdrun_hook(void *ptr1,void *ptr2) {
                                return 0;
                        }
                        steps=0;
-                       tau=mdrun->timestep;
                }
 
        }
@@ -1022,7 +1077,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
        }
 
        /* continue simulation */
-       moldyn_add_schedule(moldyn,steps,tau);
+       moldyn_add_schedule(moldyn,steps,mdrun->timestep);
 
        return 0;
 }
@@ -1108,24 +1163,27 @@ int main(int argc,char **argv) {
        set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
        switch(mdrun.lattice) {
                case FCC:
-                       create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
-                                      mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
-                                      mdrun.ly,mdrun.lz,NULL);
+                       create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
+                                      mdrun.m1,DEFAULT_ATOM_ATTR,
+                                       mdrun.fill_brand,mdrun.lx,
+                                      mdrun.ly,mdrun.lz,NULL,0,NULL);
                        break;
                case DIAMOND:
-                       create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
-                                      mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
-                                      mdrun.ly,mdrun.lz,NULL);
+                       create_lattice(&moldyn,DIAMOND,mdrun.lc,
+                                       mdrun.fill_element,
+                                      mdrun.m1,DEFAULT_ATOM_ATTR,
+                                       mdrun.fill_brand,mdrun.lx,
+                                      mdrun.ly,mdrun.lz,NULL,0,NULL);
                        break;
                case ZINCBLENDE:
                        o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
                        create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
                                       mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
-                                      mdrun.ly,mdrun.lz,&o);
+                                      mdrun.ly,mdrun.lz,&o,0,NULL);
                        o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
                        create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
                                       mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
-                                      mdrun.ly,mdrun.lz,&o);
+                                      mdrun.ly,mdrun.lz,&o,0,NULL);
                        break;
                case NONE:
                        set_nn_dist(&moldyn,mdrun.nnd);