From dc77e8ef10378188ee0a9657cedd1b7991a0a29f Mon Sep 17 00:00:00 2001
From: Samo Penic <samo@CAE-linux.(none)>
Date: Wed, 09 Apr 2014 21:27:38 +0000
Subject: [PATCH] Added spherical harmonics as-is into rbc
---
src/Makefile.am | 2
src/main.c | 2 +
src/timestep.c | 11 +++++
src/io.c | 1
src/sh.h | 1
src/tape | 5 ++
src/spherical_trisurf.c | 23 -----------
src/initial_distribution.c | 3 +
src/spherical_trisurf_ff.c | 24 ------------
src/sh.c | 25 ++++++++++++
src/io.h | 1
11 files changed, 48 insertions(+), 50 deletions(-)
diff --git a/src/Makefile.am b/src/Makefile.am
index 204da92..970dec2 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,6 +1,6 @@
trisurfdir=../
trisurf_PROGRAMS = trisurf
-trisurf_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c frame.c energy.c timestep.c vertexmove.c bondflip.c main.c poly.c stats.c
+trisurf_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c frame.c energy.c timestep.c vertexmove.c bondflip.c main.c poly.c stats.c sh.c
#trisurf_LDFLAGS = -lm -lconfuse
shdiscoverdir=../
shdiscover_PROGRAMS= shdiscover
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 0587d18..7d5647c 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -11,6 +11,7 @@
#include "energy.h"
#include "poly.h"
#include "io.h"
+#include "sh.h"
ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){
ts_fprintf(stdout,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
@@ -92,7 +93,7 @@
vesicle->pressure= tape->pressure;
vesicle->pswitch=tape->pswitch;
-
+ vesicle->sphHarmonics=sph_init(vesicle->vlist,tape->shc);
return vesicle;
}
diff --git a/src/io.c b/src/io.c
index a25b16c..d001b7e 100644
--- a/src/io.c
+++ b/src/io.c
@@ -988,6 +988,7 @@
CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
+ CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
CFG_END()
};
cfg_t *cfg;
diff --git a/src/io.h b/src/io.h
index 117c9ff..699c73e 100644
--- a/src/io.h
+++ b/src/io.h
@@ -35,6 +35,7 @@
long int inititer;
long int mcsweeps;
long int quiet;
+ long int shc;
} ts_tape;
typedef struct{
diff --git a/src/main.c b/src/main.c
index eef5835..63b72cf 100644
--- a/src/main.c
+++ b/src/main.c
@@ -11,6 +11,7 @@
#include "frame.h"
#include "timestep.h"
#include "poly.h"
+#include "sh.h"
/** Entrance function to the program
* @param argv is a number of parameters used in program call (including the program name
@@ -50,6 +51,7 @@
vesicle->dmax=tape->dmax*tape->dmax;
poly_assign_filament_xi(vesicle,tape);
vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
+ vesicle->sphHarmonics=sph_init(vesicle->vlist,tape->shc);
if(command_line_args.reset_iteration_count) start_iteration=tape->inititer;
else start_iteration++;
diff --git a/src/sh.c b/src/sh.c
index 0c4b06d..9f28d2f 100644
--- a/src/sh.c
+++ b/src/sh.c
@@ -379,3 +379,28 @@
sph->N++;
return TS_SUCCESS;
}
+
+
+ts_bool saveAvgUlm2(ts_vesicle *vesicle){
+
+ FILE *fh;
+
+ fh=fopen("sph2out.dat", "w");
+ if(fh==NULL){
+ err("Cannot open file %s for writing");
+ return TS_FAIL;
+ }
+
+ ts_spharm *sph=vesicle->sphHarmonics;
+ ts_int i,j;
+ fprintf(fh,"l,\tm,\tulm^2avg\n");
+ for(i=0;i<sph->l;i++){
+ for(j=0;j<2*i+1;j++){
+ fprintf(fh,"%d,\t%d,\t%e\n", i, j-i, sph->sumUlm2[i][j]/(ts_double)sph->N);
+
+ }
+ fprintf(fh,"\n");
+ }
+ fclose(fh);
+ return TS_SUCCESS;
+}
diff --git a/src/sh.h b/src/sh.h
index 7853139..32df46b 100644
--- a/src/sh.h
+++ b/src/sh.h
@@ -13,4 +13,5 @@
ts_bool preparationSh(ts_vesicle *vesicle, ts_double r0);
ts_bool calculateYlmi(ts_vesicle *vesicle);
ts_bool calculateUlm(ts_vesicle *vesicle);
+ts_bool saveAvgUlm2(ts_vesicle *vesicle);
#endif
diff --git a/src/spherical_trisurf.c b/src/spherical_trisurf.c
index 6c5946f..0669981 100644
--- a/src/spherical_trisurf.c
+++ b/src/spherical_trisurf.c
@@ -104,26 +104,3 @@
-ts_bool saveAvgUlm2(ts_vesicle *vesicle){
-
- FILE *fh;
-
- fh=fopen("sph2out.dat", "w");
- if(fh==NULL){
- err("Cannot open file %s for writing");
- return TS_FAIL;
- }
-
- ts_spharm *sph=vesicle->sphHarmonics;
- ts_int i,j;
- fprintf(fh,"l,\tm,\tulm^2avg\n");
- for(i=0;i<sph->l;i++){
- for(j=0;j<2*i+1;j++){
- fprintf(fh,"%d,\t%d,\t%e\n", i, j-i, sph->sumUlm2[i][j]/(ts_double)sph->N);
-
- }
- fprintf(fh,"\n");
- }
- fclose(fh);
- return TS_SUCCESS;
-}
diff --git a/src/spherical_trisurf_ff.c b/src/spherical_trisurf_ff.c
index 00a4cc0..157b0e4 100644
--- a/src/spherical_trisurf_ff.c
+++ b/src/spherical_trisurf_ff.c
@@ -87,27 +87,3 @@
}
-
-ts_bool saveAvgUlm2(ts_vesicle *vesicle){
-
- FILE *fh;
-
- fh=fopen("sph2out.dat", "w");
- if(fh==NULL){
- err("Cannot open file %s for writing");
- return TS_FAIL;
- }
-
- ts_spharm *sph=vesicle->sphHarmonics;
- ts_int i,j;
- fprintf(fh,"l,\tm,\tulm^2avg\n");
- for(i=0;i<sph->l;i++){
- for(j=0;j<2*i+1;j++){
- fprintf(fh,"%d,\t%d,\t%e\n", i, j-i, sph->sumUlm2[i][j]/(ts_double)sph->N);
-
- }
- fprintf(fh,"\n");
- }
- fclose(fh);
- return TS_SUCCESS;
-}
diff --git a/src/tape b/src/tape
index dbaabdb..833acaa 100644
--- a/src/tape
+++ b/src/tape
@@ -48,9 +48,12 @@
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
inititer=0
#how many records do you want on the disk iteration are there in a run?
-iterations=20
+iterations=2000
+###### Spherical harmonics ###########
+spherical_harmonics_coefficients=21
+
#shut up if we are using cluster!!!
quiet=false
diff --git a/src/timestep.c b/src/timestep.c
index 9ab60fd..c61099b 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -9,9 +9,12 @@
#include "frame.h"
#include "io.h"
#include "stats.h"
+#include "sh.h"
+#include "vesicle.h"
ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations, ts_uint start_iteration){
ts_uint i, j;
+ ts_double r0;
ts_double l1,l2,l3,volume=0.0,area=0.0,vmsr,bfsr, vmsrt, bfsrt;
ts_ulong epochtime;
// char filename[255];
@@ -43,6 +46,14 @@
epochtime=get_epoch();
gyration_eigen(vesicle, &l1, &l2, &l3);
get_area_volume(vesicle, &area,&volume);
+ vesicle_volume(vesicle);
+ r0=getR0(vesicle);
+ preparationSh(vesicle,r0);
+ calculateYlmi(vesicle);
+ calculateUlm(vesicle);
+ storeUlm2(vesicle);
+ saveAvgUlm2(vesicle);
+
fprintf(fd, "%lu %u %e %e %e %e %e %e %e\n",epochtime,i,vmsr,bfsr,volume, area,l1,l2,l3);
// sprintf(filename,"timestep-%05d.pov",i-inititer);
--
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