From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Tue, 29 Apr 2008 09:23:17 +0000 (+0200)
Subject: fixed compile errors, no testing yet!
X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=3592f3b0cf641729566674a7cdfd8eff3f61f59a;p=physik%2Fposic.git

fixed compile errors, no testing yet!
---

diff --git a/config.default b/config.default
index 0bd26d2..e9181be 100644
--- a/config.default
+++ b/config.default
@@ -22,14 +22,6 @@ pbc 1 1 1
 temperature 450.0
 pressure 0.0
 
-## ensemble control ##
-
-ectrl 100.0 100.0
-
-## equi ctrl ##
-
-equictrl 1.0 1.0
-
 ## initial lattice ##
 
 lattice diamond
@@ -38,31 +30,25 @@ element1 silicon
 #element2 carbon
 fill lc 9 9 9
 
-aattr all h
+## atom attributes ##
+
+aattr t h123
 
 ## initial simulation run ##
 
 prerun 100
 avgskip 0
 
-## more stages ##
+## system attributes, eg ensemble ctrl, equi ctrl, relaxation steps ##
 
-# format:
-# stage <action> <attr>
-#
-# actions:
-#
-# ins_atoms <#insertions> <#atoms> <element> \
-#           <#atom-attrib> <position>
-#
-# continue <#runs>
-#
-# anneal <#annealing-steps> <delta_t>
+sattr pctrl 100.0 tctrl 100.0 prelax 1.0 trelax 1.0 rsteps 100 avgrst 1
+
+## more stages ##
 
-stage ins_atoms 10 1 14 v h rand 0 0 0 11 11 11
-stage ins_atoms 1 1 6 v h rand 0 0 0 5.429 5.429 5.429
+stage ins_atoms 10 1 14 0 vh123 rand -5.5 -5.5 -5.5 5.5 5.5 5.5
+stage ins_atoms 1 1 6 1 vh123 rand 0 0 0 5.429 5.429 5.429
 stage continue 10000
-stage anneal 723 -1.0
+#stage anneal 723 -1.0
 
 ## report / log / visualization / save files ##
 
diff --git a/mdrun.c b/mdrun.c
index 6f7a2f0..c4b6df2 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -62,12 +62,12 @@ int mdrun_parse_argv(t_mdrun *mdrun,int argc,char **argv) {
 	return 0;
 }
 
-del_stages(t_mdrun *mdrun) {
+int del_stages(t_mdrun *mdrun) {
 
 	t_list *sl;
 	t_stage *stage;
 
-	sl=mdrun->stage;
+	sl=&(mdrun->stage);
 
 	list_reset_f(sl);
 
@@ -83,7 +83,7 @@ del_stages(t_mdrun *mdrun) {
 	return 0;
 }
 
-add_stage(t_mdrun *mdrun,u8 type,void *params) {
+int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 
 	int psize;
 
@@ -106,7 +106,8 @@ add_stage(t_mdrun *mdrun,u8 type,void *params) {
 			psize=sizeof(t_chsattr_params);
 			break;
 		default:
-
+			printf("%s unknown stage type: %02x\n",ME,type);
+			return -1;
 	}
 
 	stage=malloc(sizeof(t_stage));
@@ -126,7 +127,7 @@ add_stage(t_mdrun *mdrun,u8 type,void *params) {
 
 	memcpy(stage->params,params,psize);
 
-	list_add_immediate_f(mdrun->stage,stage);
+	list_add_immediate_f(&(mdrun->stage),stage);
 
 	return 0;
 }
@@ -168,6 +169,13 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 		if((line[0]=='#')|(ret==1))
 			continue;
 
+		// reset
+		memset(&iap,0,sizeof(t_insert_atoms_params));
+		memset(&cp,0,sizeof(t_continue_params));
+		memset(&ap,0,sizeof(t_anneal_params));
+		memset(&cap,0,sizeof(t_chaattr_params));
+		memset(&csp,0,sizeof(t_chsattr_params));
+
 		// get command + args
 		wcnt=0;
 		while(1) {
@@ -271,13 +279,37 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 		else if(!strncmp(word[0],"aattr",5)) {
 			// for aatrib line we need a special stage
 			// containing one schedule of 0 loops ...
-			if(!strncmp(word[1],"all",3)) {
-				cap.type=
-
-
-				HIER WEITER
+			for(i=0;i<strlen(word[1]);i++) {
+				switch(word[1][i]) {
+					case 't':
+						cap.type|=CHAATTR_TOTALV;
+						break;
+					case 'r':
+						cap.type|=CHAATTR_REGION;
+						break;
+					case 'e':
+						cap.type|=CHAATTR_ELEMENT;
+						break;
+					default:
+						break;
+				}
+			}
+			i=1;
+			if(cap.type&CHAATTR_REGION) {
+				cap.x0=atof(word[1]);	
+				cap.y0=atof(word[2]);	
+				cap.z0=atof(word[3]);	
+				cap.x1=atof(word[4]);	
+				cap.y1=atof(word[5]);	
+				cap.z1=atof(word[6]);
+				i+=6;
 			}
-			for(i=0;i<strlen(wptr)) {
+			if(cap.type&CHAATTR_ELEMENT) {
+				cap.element=atoi(word[i]);
+				i+=1;
+			}
+			wptr=word[i];
+			for(i=0;i<strlen(wptr);i++) {
 				switch(word[2][i]) {
 					case 'b':
 						cap.attr|=ATOM_ATTR_VB;
@@ -306,9 +338,30 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 			}
 			add_stage(mdrun,STAGE_CHAATTR,&cap);
 		}
-		else if(!strncmp(word[0],"ectrl",5)) {
-			mdrun->p_tau=atof(word[1]);
-			mdrun->t_tau=atof(word[2]);
+		else if(!strncmp(word[0],"sattr",5)) {
+			// for satrib line we need a special stage
+			// containing one schedule of 0 loops ...
+			for(i=1;i<wcnt;i++) {
+				if(!strncmp(word[i],"pctrl",5)) {
+					csp.ptau=atof(word[++i]);
+				}
+				if(!strncmp(word[i],"tctrl",5)) {
+					csp.ttau=atof(word[++i]);
+				}
+				if(!strncmp(word[i],"prelax",6)) {
+					csp.dp=atof(word[++i]);
+				}
+				if(!strncmp(word[i],"trelax",6)) {
+					csp.dt=atof(word[++i]);
+				}
+				if(!strncmp(word[i],"rsteps",6)) {
+					csp.rsteps=atoi(word[++i]);
+				}
+				if(!strncmp(word[i],"avgrst",6)) {
+					csp.avgrst=atoi(word[++i]);
+				}
+			}
+			add_stage(mdrun,STAGE_CHSATTR,&csp);
 		}
 		else if(!strncmp(word[0],"prerun",6))
 			mdrun->prerun=atoi(word[1]);
@@ -328,10 +381,72 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 			mdrun->visualize=atoi(word[1]);
 		else if(!strncmp(word[0],"stage",5)) {
 			// for every stage line, add a stage
-			printf("%s stage: %s\n",ME,word[1]);
+			if(!strncmp(word[1],"ins_atoms",9)) {
+				iap.ins_steps=atoi(word[2]);
+				iap.ins_atoms=atoi(word[3]);
+				iap.element=atoi(word[4]);
+				iap.element=atoi(word[4]);
+				iap.brand=atoi(word[5]);
+				for(i=0;i<strlen(word[6]);i++) {
+					switch(word[6][i]) {
+						case 'b':
+							iap.attr|=ATOM_ATTR_VB;
+							break;
+						case 'h':
+							iap.attr|=ATOM_ATTR_HB;
+							break;
+						case 'v':
+							iap.attr|=ATOM_ATTR_VA;
+							break;
+						case 'f':
+							iap.attr|=ATOM_ATTR_FP;
+							break;
+						case '1':
+							iap.attr|=ATOM_ATTR_1BP;
+							break;
+						case '2':
+							iap.attr|=ATOM_ATTR_2BP;
+							break;
+						case '3':
+							iap.attr|=ATOM_ATTR_3BP;
+							break;
+						default:
+							break;
+					}
+				}
+				// only rand mode by now
+				if(word[8][0]=='t')
+					iap.type=INS_TOTAL;
+				else {
+					iap.type=INS_REGION;
+					iap.x0=atof(word[8]);
+					iap.y0=atof(word[9]);
+					iap.z0=atof(word[10]);
+					iap.x1=atof(word[11]);
+					iap.y1=atof(word[12]);
+					iap.z1=atof(word[13]);
+				}
+				add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
+			}
+			else if(!strncmp(word[1],"continue",8)) {
+				cp.runs=atoi(word[2]);
+				add_stage(mdrun,STAGE_CONTINUE,&cp);
+			}
+			else if(!strncmp(word[1],"anneal",6)) {
+				ap.count=0;
+				ap.runs=atoi(word[2]);
+				ap.dt=atof(word[3]);
+				add_stage(mdrun,STAGE_ANNEAL,&ap);
+			}
+			else {
+				printf("%s unknown stage type: %s\n",
+				       ME,word[1]);
+				return -1;
+			}
 		}
 		else {
-			printf("%s unknown command %s, skipped!\n",ME,word[0]);
+			printf("%s unknown keyword '%s', skipped!\n",
+			       ME,word[0]);
 			continue;
 		}
 	}
@@ -380,7 +495,7 @@ int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 
 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 
-	insert_atoms_params *iap;
+	t_insert_atoms_params *iap;
 	t_stage *stage;
 	t_atom *atom;
 	t_3dvec r,v,dist;
@@ -390,7 +505,7 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 	double x0,y0,z0;
 	u8 cr_check,run;
 	
-	stage=mdrun->stage->current->data;
+	stage=mdrun->stage.current->data;
 	iap=stage->params;
 
 	cr_check=FALSE;
@@ -417,7 +532,8 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 			cr_check=TRUE;
 			break;
 		default:
-			printf("%s unknown insertion mode\n");
+			printf("%s unknown insertion mode: %02x\n",
+			       ME,iap->type);
 			return -1;
 	}
 
@@ -455,14 +571,14 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 	return 0;
 }
 
-int chaatrib(t_moldyn *moldyn,t_mdrun *mdrun) {
+int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 
 	t_stage *stage;
 	t_chaattr_params *cap;
 	t_atom *atom;
-	u8 assigne;
+	int i;
 
-	stage=mdrun->stage->current->data;
+	stage=mdrun->stage.current->data;
 	cap=stage->params;
 
 	for(i=0;i<moldyn->count;i++) {
@@ -496,41 +612,51 @@ int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 	t_stage *stage;
 	t_chsattr_params *csp;
 
-	stage=mdrun->stage->current->data;
+	stage=mdrun->stage.current->data;
 	csp=stage->params;
 
-	switch(csp->type) {
-		case CHSATTR_PCTRL:
-			set_p_scale(moldyn,csp->ctrl_type,csp->tau);
-			break;
-		case CHSATTR_TCTRL:
-			set_t_scale(moldyn,csp->ctrl_type,csp->tau);
-			break;
-		case CHSATTR_PRELAX:
-			mdrun->sattr&=(^(SATTR_PRELAX));
-			if(csp->ctrl==TRUE)
-				mdrun->sattr|=SATTR_PRELAX;
-			break;
-		case CHSATTR_TRELAX:
-			mdrun->sattr&=(^(SATTR_TRELAX));
-			if(csp->ctrl==TRUE)
-				mdrun->sattr|=SATTR_TRELAX;
-			break;
-		case CHSATTR_AVGRST:
-			mdrun->sattr&=(^(SATTR_AVGRST));
-			if(csp->ctrl==TRUE)
-				mdrun->sattr|=SATTR_AVGRST;
-			break;
-		default:
-			printf("%s unknown system attribute change\n",ME);
-			return -1;
+	if(csp->type&CHSATTR_PCTRL) {
+		if(csp->ptau>0)
+			set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
+		else
+			set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
+	}
+	if(csp->type&CHSATTR_TCTRL) {
+		if(csp->ttau>0)
+			set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
+		else
+			set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
+	}
+	if(csp->type&CHSATTR_PRELAX) {
+		if(csp->dp<0)
+			mdrun->sattr&=(~(SATTR_PRELAX));
+		else
+			mdrun->sattr|=SATTR_PRELAX;
+		mdrun->dp=csp->dp;
+	}
+	if(csp->type&CHSATTR_TRELAX) {
+		if(csp->dt<0)
+			mdrun->sattr&=(~(SATTR_TRELAX));
+		else
+			mdrun->sattr|=SATTR_TRELAX;
+		mdrun->dt=csp->dt;
+	}
+	if(csp->type&CHSATTR_AVGRST) {
+		if(csp->avgrst)
+			mdrun->sattr|=CHSATTR_AVGRST;
+		else
+			mdrun->sattr&=(~(CHSATTR_AVGRST));
+	}
+	if(csp->type&CHSATTR_RSTEPS) {
+		mdrun->relax_steps=csp->rsteps;
 	}
 
 	return 0;
 }
 
-int mdrun_hook(t_moldyn *moldyn,void *ptr) {
+int mdrun_hook(void *ptr1,void *ptr2) {
 
+	t_moldyn *moldyn;
 	t_mdrun *mdrun;
 	t_stage *stage;
 	t_list *sl;
@@ -542,8 +668,10 @@ int mdrun_hook(t_moldyn *moldyn,void *ptr) {
 	t_continue_params *cp;
 	t_anneal_params *ap;
 
-	mdrun=ptr;
-	sl=mdrun->stage;
+	moldyn=ptr1;
+	mdrun=ptr2;
+
+	sl=&(mdrun->stage);
 
 	change_stage=FALSE;
 
@@ -552,14 +680,15 @@ int mdrun_hook(t_moldyn *moldyn,void *ptr) {
 		return 0;
 
 	/* get stage description */
-	stage=mdrun->sl->current->data;
+	stage=sl->current->data;
 
 	/* default steps and tau values */
 	steps=mdrun->relax_steps;
 	tau=mdrun->timestep;
 
 	/* check whether relaxation steps are necessary */
-	if(!((check_pressure==FALSE)|(check_temperature==FALSE))) {
+	if(!((check_pressure(moldyn,mdrun)==FALSE)|\
+	     (check_temperature(moldyn,mdrun)==FALSE))) {
 		
 		/* stage specific stuff */
 		switch(stage->type) {
@@ -590,11 +719,11 @@ int mdrun_hook(t_moldyn *moldyn,void *ptr) {
 				ap->count+=1;
 				break;
 			case STAGE_CHAATTR:
-				chaatrib(moldyn,mdrun);
+				chaatr(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
 			case STAGE_CHSATTR:
-				chsatrib(moldyn,mdrun);
+				chsattr(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
 			default:
@@ -704,7 +833,7 @@ int main(int argc,char **argv) {
 			               mdrun.ly,mdrun.lz,&o);
 			o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
-			               mdrun.m2,0,0,mdrun.lx,
+			               mdrun.m2,0,1,mdrun.lx,
 			               mdrun.ly,mdrun.lz,&o);
 			break;
 		default:
@@ -734,12 +863,6 @@ int main(int argc,char **argv) {
 	moldyn_set_log(&moldyn,CREATE_REPORT,0);
 	set_avg_skip(&moldyn,mdrun.avgskip);
 
-	/* pt scaling */
-	if(mdrun.p_tau!=0)
-		set_p_scale(&moldyn,P_SCALE_BERENDSEN,mdrun.p_tau);
-	if(mdrun.t_tau!=0)
-		set_t_scale(&moldyn,T_SCALE_BERENDSEN,mdrun.t_tau);
-
 	/* prepare the hook function */
 	moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
 
diff --git a/mdrun.h b/mdrun.h
index be8e2a4..20d68d7 100644
--- a/mdrun.h
+++ b/mdrun.h
@@ -11,12 +11,16 @@
 #include <sys/types.h>
 #include <sys/stat.h>
 #include <fcntl.h>
+#include <unistd.h>
 
 #include <math.h>
 
 /* main molecular dynamics api */
 #include "moldyn.h"
 
+/* elements */
+#include "pse.h"
+
 /* list api */
 #include "list/list.h"
 
@@ -73,10 +77,8 @@ typedef struct s_mdrun {
 	u8 sattr;				// system attributes
 	double temperature;			// temperature
 	double pressure;			// pressure
-	double p_tau;				// pressure tau
-	double t_tau;				// temperature tau
-	double dp;				// delta p fpr pctrl
-	double dt;				// delta t for tctrl
+	double dp;
+	double dt;
 	int relax_steps;			// amount of relaxation steps
 
 	int prerun;				// amount of loops in first run
@@ -91,7 +93,7 @@ typedef struct s_mdrun {
 	int avgskip;				// average skip
 	char sdir[128];				// save root
 
-	t_list *stage;				// stages
+	t_list stage;				// stages
 	int s_cnt;				// stage counter
 } t_mdrun;
 
@@ -108,7 +110,7 @@ typedef struct s_insert_atoms_params {
 	int ins_atoms;
 	int element;
 	u8 brand;
-	u8 aattr;
+	u8 attr;
 } t_insert_atoms_params;
 
 #define INS_TOTAL				0x01
@@ -138,9 +140,12 @@ typedef struct s_chaattr_params {
 
 typedef struct s_chsattr_params {
 	u8 type;
-	double tau;
-	u8 ctrl;
-	double delta;
+	double ttau;
+	double ptau;
+	double dt;
+	double dp;
+	int rsteps;
+	u8 avgrst;
 } t_chsattr_params;
 
 #define CHSATTR_PCTRL				0x01
@@ -148,6 +153,7 @@ typedef struct s_chsattr_params {
 #define CHSATTR_PRELAX				0x04
 #define CHSATTR_TRELAX				0x08
 #define CHSATTR_AVGRST				0x10
+#define CHSATTR_RSTEPS				0x20
 
 /*
  * function prototypes
diff --git a/moldyn.c b/moldyn.c
index 988b467..832d171 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -79,7 +79,8 @@ static char *pse_col[]={
 	"Ar",
 };
 
-static double *pse_mass[]={
+/*
+static double pse_mass[]={
 	0,
 	0,
 	0,
@@ -101,7 +102,7 @@ static double *pse_mass[]={
 	0,
 };
 
-static double *pse_lc[]={
+static double pse_lc[]={
 	0,
 	0,
 	0,
@@ -122,6 +123,7 @@ static double *pse_lc[]={
 	0,
 	0,
 };
+*/
 
 /*
  * the moldyn functions
@@ -202,7 +204,7 @@ int set_pressure(t_moldyn *moldyn,double p_ref) {
 
 int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc) {
 
-	moldyn->pt_scalei&=(^(P_SCALE_MASK));
+	moldyn->pt_scale&=(~(P_SCALE_MASK));
 	moldyn->pt_scale|=ptype;
 	moldyn->p_tc=ptc;
 
@@ -213,27 +215,17 @@ int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc) {
 		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;
 }
 
 int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc) {
 
-	moldyn->pt_scalei&=(^(T_SCALE_MASK));
+	moldyn->pt_scale&=(~(T_SCALE_MASK));
 	moldyn->pt_scale|=ttype;
 	moldyn->t_tc=ttc;
 
 	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);