cleaning + set hook function

diff --git a/moldyn.c b/moldyn.c
index d33de02efa776fa52dd3a10bbd5ca00d93ba7b4c..9db5cd9053fea64ce0cc5bd09cc667caa360bd4a 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -19,6 +19,8 @@
 
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
+       printf("[moldyn] init\n");
+
        memset(moldyn,0,sizeof(t_moldyn));
 
        rand_init(&(moldyn->random),NULL,1);
@@ -30,6 +32,7 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 int moldyn_shutdown(t_moldyn *moldyn) {
 
        printf("[moldyn] shutdown\n");
+
        moldyn_log_shutdown(moldyn);
        link_cell_shutdown(moldyn);
        rand_close(&(moldyn->random));
@@ -40,12 +43,16 @@ int moldyn_shutdown(t_moldyn *moldyn) {
 
 int set_int_alg(t_moldyn *moldyn,u8 algo) {
 
+       printf("[moldyn] integration algorithm: ");
+
        switch(algo) {
                case MOLDYN_INTEGRATE_VERLET:
                        moldyn->integrate=velocity_verlet;
+                       printf("velocity verlet\n");
                        break;
                default:
                        printf("unknown integration algorithm: %02x\n",algo);
+                       printf("unknown\n");
                        return -1;
        }
 
@@ -56,6 +63,8 @@ int set_cutoff(t_moldyn *moldyn,double cutoff) {
 
        moldyn->cutoff=cutoff;
 
+       printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
+
        return 0;
 }
 
@@ -63,6 +72,8 @@ int set_temperature(t_moldyn *moldyn,double t_ref) {
 
        moldyn->t_ref=t_ref;
 
+       printf("[moldyn] temperature: %f\n",moldyn->t_ref);
+
        return 0;
 }
 
@@ -70,6 +81,8 @@ int set_pressure(t_moldyn *moldyn,double p_ref) {
 
        moldyn->p_ref=p_ref;
 
+       printf("[moldyn] pressure: %f\n",moldyn->p_ref);
+
        return 0;
 }
 
@@ -79,6 +92,18 @@ int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
        moldyn->t_tc=ttc;
        moldyn->p_tc=ptc;
 
+       printf("[moldyn] p/t scaling:\n");
+
+       printf("  p: %s",ptype?"yes":"no ");
+       if(ptype)
+               printf(" | type: %02x | factor: %f",ptype,ptc);
+       printf("\n");
+
+       printf("  t: %s",ttype?"yes":"no ");
+       if(ttype)
+               printf(" | type: %02x | factor: %f",ttype,ttc);
+       printf("\n");
+
        return 0;
 }
 
@@ -101,7 +126,7 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
        printf("  y: %f\n",moldyn->dim.y);
        printf("  z: %f\n",moldyn->dim.z);
        printf("  volume: %f\n",moldyn->volume);
-       printf("  visualize simulation box: %s\n",visualize?"on":"off");
+       printf("  visualize simulation box: %s\n",visualize?"yes":"no");
 
        return 0;
 }
@@ -115,6 +140,8 @@ int set_nn_dist(t_moldyn *moldyn,double dist) {
 
 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 
+       printf("[moldyn] periodic boundary conditions:\n");
+
        if(x)
                moldyn->status|=MOLDYN_STAT_PBX;
 
@@ -124,6 +151,10 @@ int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
        if(z)
                moldyn->status|=MOLDYN_STAT_PBZ;
 
+       printf("  x: %s\n",x?"yes":"no");
+       printf("  y: %s\n",y?"yes":"no");
+       printf("  z: %s\n",z?"yes":"no");
+
        return 0;
 }
 
@@ -171,6 +202,8 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
        char filename[128];
        int ret;
 
+       printf("[moldyn] set log: ");
+
        switch(type) {
                case LOG_TOTAL_ENERGY:
                        moldyn->ewrite=timer;
@@ -183,6 +216,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
                                return moldyn->efd;
                        }
                        dprintf(moldyn->efd,"# total energy log file\n");
+                       printf("total energy (%d)\n",timer);
                        break;
                case LOG_TOTAL_MOMENTUM:
                        moldyn->mwrite=timer;
@@ -195,9 +229,11 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
                                return moldyn->mfd;
                        }
                        dprintf(moldyn->efd,"# total momentum log file\n");
+                       printf("total momentum (%d)\n",timer);
                        break;
                case SAVE_STEP:
                        moldyn->swrite=timer;
+                       printf("save file (%d)\n",timer);
                        break;
                case VISUAL_STEP:
                        moldyn->vwrite=timer;
@@ -206,9 +242,10 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
                                printf("[moldyn] visual init failure\n");
                                return ret;
                        }
+                       printf("visual file (%d)\n",timer);
                        break;
                default:
-                       printf("[moldyn] unknown log mechanism: %02x\n",type);
+                       printf("unknown log type: %02x\n",type);
                        return -1;
        }
 
@@ -429,6 +466,8 @@ int thermal_init(t_moldyn *moldyn,u8 equi_init) {
        atom=moldyn->atom;
        random=&(moldyn->random);
 
+       printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
+
        /* gaussian distribution of velocities */
        v3_zero(&p_total);
        for(i=0;i<moldyn->count;i++) {
@@ -846,10 +885,14 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
        schedule->tau=ptr;
        schedule->tau[count-1]=tau;
 
+       printf("[moldyn] schedule added:\n");
+       printf("  number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
+                                      
+
        return 0;
 }
 
-int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
+int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
 
        moldyn->schedule.hook=hook;
        moldyn->schedule.hook_params=hook_params;
@@ -912,6 +955,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
        /* debugging, ignore */
        moldyn->debug=0;
 
+       /* tell the world */
+       printf("[moldyn] integration start, go get a coffee ...\n");
+
        /* executing the schedule */
        for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
 
@@ -1199,9 +1245,9 @@ printf("\n\n");
        for(i=0;i<count;i++)
                moldyn->vt2-=v3_scalar_product(&(itom[i].r),&(itom[i].f));
 
-printf("compare: vt1: %f vt2: %f\n",moldyn->vt1,moldyn->vt2);
+//printf("compare: vt1: %f vt2: %f\n",moldyn->vt1,moldyn->vt2);
 
-pressure_calc(moldyn);
+//pressure_calc(moldyn);
 
        return 0;
 }

diff --git a/moldyn.h b/moldyn.h
index c5cc064cedc85c1cd417b8b65a7f20fb74c44311..8254568af609f69d171862a7ba9d8023bee8decc 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -71,7 +71,7 @@ typedef struct s_moldyn_schedule {
        int total_sched;
        int *runs;
        double *tau;
-       int (*hook)(void *moldyn,void *hook);
+       int (*hook)(void *moldyn,void *hook_params);
        void *hook_params;
 } t_moldyn_schedule;
 
@@ -422,8 +422,10 @@ int link_cell_update(t_moldyn *moldyn);
 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
 int link_cell_shutdown(t_moldyn *moldyn);
 
+typedef int (*set_hook)(void *,void *);
+
 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
-int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params);
+int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
 
 int moldyn_integrate(t_moldyn *moldyn);
 int velocity_verlet(t_moldyn *moldyn);

diff --git a/run b/run
index 5a3a76896c8fc7fcdb3c0690f2560ca8a5b485fe..5a20df0b0acb4ce0266fe158db475901f163aa3f 100755 (executable)
--- a/run
+++ b/run
@@ -1,4 +1,4 @@
-mkdir -p saves video
+[ ! -d $1 ] && mkdir $1
 ./clean $1
 ./sic $@
 if [ "$?" == "0" ]; then

diff --git a/sic.c b/sic.c
index e2e86262627b76a91ee3d243e01435e5f0ca6824..a890270fede20f6080fec30a8f3f9b63af997c16 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -11,6 +11,18 @@
 
 #include "posic.h"
 
+int hook(void *moldyn,void *hook_params) {
+
+       t_moldyn *md;
+
+       md=moldyn;
+
+       /* decrease temperature in every hook */
+       set_temperature(md,md->t_ref-100.0);
+
+       return 0;
+}
+
 int main(int argc,char **argv) {
 
        /* check argv */
@@ -27,25 +39,16 @@ int main(int argc,char **argv) {
        t_ho_params ho;
        t_tersoff_mult_params tp;
 
-       /* misc parameters */
-       double tau;
-
        /* testing location & velocity vector */
        t_3dvec r,v;
 
-       /* values */
-       tau=1.0e-15;    /* delta t = 1 fs */
-
        /* initialize moldyn */
-       printf("[sic] moldyn init\n");
        moldyn_init(&md,argc,argv);
 
        /* choose integration algorithm */
-       printf("[sic] setting integration algorithm\n");
        set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 
        /* choose potential */
-       printf("[sic] selecting potential\n");
        //set_potential1b(&md,tersoff_mult_1bp,&tp);
        //set_potential2b(&md,tersoff_mult_2bp,&tp);
        //set_potential2b_post(&md,tersoff_mult_post_2bp,&tp);
@@ -54,9 +57,8 @@ int main(int argc,char **argv) {
        //set_potential2b(&md,harmonic_oscillator,&ho);
 
        /* cutoff radius */
-       printf("[sic] setting cutoff radius\n");
        //set_cutoff(&md,TM_S_SI);
-       set_cutoff(&md,3*LC_SI);
+       set_cutoff(&md,2*LC_SI);
 
        /*
         * potential parameters
@@ -105,19 +107,16 @@ int main(int argc,char **argv) {
        tersoff_mult_complete_params(&tp);
 
        /* set (initial) dimensions of simulation volume */
-       printf("[sic] setting dimensions\n");
-       set_dim(&md,10*LC_SI,10*LC_SI,10*LC_SI,TRUE);
+       set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
 
        /* set periodic boundary conditions in all directions */
-       printf("[sic] setting periodic boundary conditions\n");
        set_pbc(&md,TRUE,TRUE,TRUE);
 
        /* create the lattice / place atoms */
-       printf("[sic] creating atoms\n");
        create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
        //               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
                       ATOM_ATTR_2BP|ATOM_ATTR_HB,
-                      0,10,10,10);
+                      0,6,6,6);
        moldyn_bc_check(&md);
 
        /* testing configuration */
@@ -141,7 +140,6 @@ int main(int argc,char **argv) {
        set_nn_dist(&md,0.25*sqrt(3.0)*LC_SI); /* diamond ! */
 
        /* set temperature */
-       printf("[sic] setting temperature -> %f\n",273+atof(argv[2]));
        //set_temperature(&md,273.0+1410.0);
        //set_temperature(&md,273.0+450.0);
        //set_temperature(&md,273.0);
@@ -150,42 +148,43 @@ int main(int argc,char **argv) {
        set_temperature(&md,atof(argv[2])+273.0);
 
        /* set pressure */
-       printf("[sic] setting pressure\n");
        set_pressure(&md,ATM);
 
        /* set p/t scaling */
-       printf("[sic] set p/t scaling\n");
        //set_pt_scale(&md,P_SCALE_BERENDSEN,100.0,
        //                 T_SCALE_BERENDSEN,100.0);
-       //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
+       set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
        //set_pt_scale(&md,P_SCALE_BERENDSEN,100.0,0,0);
        
        /* initial thermal fluctuations of particles (in equilibrium) */
-       printf("[sic] thermal init\n");
        thermal_init(&md,TRUE);
 
        /* create the simulation schedule */
-       printf("[sic] adding schedule\n");
-       moldyn_add_schedule(&md,10001,1.0);
+       moldyn_add_schedule(&md,100,1.0);
+       moldyn_add_schedule(&md,100,1.0);
+       moldyn_add_schedule(&md,100,1.0);
+       moldyn_add_schedule(&md,100,1.0);
+       moldyn_add_schedule(&md,100,1.0);
+       moldyn_add_schedule(&md,100,1.0);
+       moldyn_add_schedule(&md,100,1.0);
+       moldyn_add_schedule(&md,100,1.0);
+
+       /* schedule hook function */
+       moldyn_set_schedule_hook(&md,&hook,NULL);
 
        /* activate logging */
-       printf("[sic] activate logging\n");
        moldyn_set_log_dir(&md,argv[1]);
-       moldyn_set_log(&md,LOG_TOTAL_ENERGY,10);
-       moldyn_set_log(&md,VISUAL_STEP,100);
+       moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
+       moldyn_set_log(&md,VISUAL_STEP,10);
 
        /*
         * let's do the actual md algorithm now
         *
         * integration of newtons equations
         */
-
-       printf("[sic] integration start, go get a coffee ...\n");
        moldyn_integrate(&md);
 
        /* close */
-
-       printf("[sic] shutdown\n");
        moldyn_shutdown(&md);
        
        return 0;