From 3f5658c8e3ac0b1febafe06c81c334f9b31a73be Mon Sep 17 00:00:00 2001 From: Samo Penic <samo.penic@fe.uni-lj.si> Date: Tue, 24 May 2016 20:20:07 +0000 Subject: [PATCH] Merge branch 'master' of bitbucket.org:samop/trisurf-ng --- /dev/null | 40 -------------------- configure.ac | 3 - src/tape | 8 ++-- python/setup.py | 9 ++++ python/MANIFEST.in | 1 Makefile.am | 2 build.sh | 4 + src/restore.c | 15 ++++++- 8 files changed, 31 insertions(+), 51 deletions(-) diff --git a/Makefile.am b/Makefile.am index c543989..1bfdcf4 100644 --- a/Makefile.am +++ b/Makefile.am @@ -1 +1 @@ -SUBDIRS=test src +SUBDIRS=src diff --git a/bin/trisurf-deploy b/bin/trisurf-deploy deleted file mode 100755 index 06b54da..0000000 --- a/bin/trisurf-deploy +++ /dev/null @@ -1,48 +0,0 @@ -#!/bin/bash - -#This part is a configuration part of trisurf deploy - - -#definition of tapes -declare -a tapes=("tape1" "tape2" "tape3" "tape4"); - -#what options from tape should be overriden -declare -a tape_overrides=("xk0=10" "constvol=2,xk=20" "" ""); - -#some extra options for program execution -declare -a extra_options=("--force-from-tape" "--reset-iteration-count" "" ""); - -#main directory -declare directory="/home/samo/trisurfanje" - -#subdirectory structure -function subdir() { - - echo "ABC"; -} - - -#End of configuration - -declare tape_no=${#tapes[@]} -for i in `seq 1 $tape_no`; do - declare sdir=$(subdir) - declare dir_struct="$directory/$sdir" -#if doesnt exist - echo "mkdir $dir_struct" -#if doesnt exist - echo "cp ${tapes[i-1]} $dir_struct" - - - echo "trisurf -t ${tapes[i-1]} -d $dir_struct -o ${tape_overrides[i-1]} ${extra_options[i-1]}" -done; - - -#Functions required for operation - - -echo "Deploying configuration of trisurf" - - - - diff --git a/build.sh b/build.sh index 2ac3b5a..a587e47 100755 --- a/build.sh +++ b/build.sh @@ -8,4 +8,6 @@ make clean make sudo make install - +cd python +sudo python3 setup.py install +cd .. diff --git a/configure.ac b/configure.ac index f43881a..09b04d8 100644 --- a/configure.ac +++ b/configure.ac @@ -51,6 +51,5 @@ AC_CHECK_FUNCS([pow sqrt strndup]) AC_CONFIG_FILES([Makefile - src/Makefile - test/Makefile]) + src/Makefile]) AC_OUTPUT diff --git a/python/MANIFEST.in b/python/MANIFEST.in new file mode 100644 index 0000000..73b9b6d --- /dev/null +++ b/python/MANIFEST.in @@ -0,0 +1 @@ +recursive-include trisurf *.py diff --git a/python/setup.py b/python/setup.py new file mode 100644 index 0000000..fb98073 --- /dev/null +++ b/python/setup.py @@ -0,0 +1,9 @@ +from distutils.core import setup + +setup(name="trisurf", version="0.1a", +description="Python trisurf-ng managing scripts for organized multiple runs of simultations", +author="Samo Penic", +author_email="samo.penic@gmail.com", +url="", +packages=["trisurf"] +) diff --git a/src/restore.c b/src/restore.c index 8f985de..6edb848 100644 --- a/src/restore.c +++ b/src/restore.c @@ -287,7 +287,7 @@ xmlNodePtr child = cur->xmlChildrenNode; xmlChar *points; char *pts; - int i, idx, polyidx, monoidx; + int i, idx, polyidx, monoidx, filidx, fonoidx; char *token[3]; while (child != NULL) { if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){ @@ -302,12 +302,19 @@ vesicle->vlist->vtx[idx]->x=atof(token[0]); vesicle->vlist->vtx[idx]->y=atof(token[1]); vesicle->vlist->vtx[idx]->z=atof(token[2]); - } else { + } else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) { polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono; monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono; vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->x=atof(token[0]); vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->y=atof(token[1]); vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->z=atof(token[2]); + } else { + filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono; + fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono; + fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]); + vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->x=atof(token[0]); + vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->y=atof(token[1]); + vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->z=atof(token[2]); } for(i=0;i<2;i++) token[i]=strtok(NULL," "); token[2]=strtok(NULL,"\n"); @@ -317,6 +324,7 @@ } child=child->next; } + fprintf(stderr,"Came here\n"); //fprintf(stderr,"Vertices position j=%d\n",idx); return TS_SUCCESS; @@ -341,7 +349,8 @@ } else { //find grafted vtx - if((vesicle->tape->nmono-1)==(idx-3*(vesicle->vlist->n-2))%(vesicle->tape->nmono)){ + if(vesicle->tape->npoly && vesicle->tape->nmono && (vesicle->tape->nmono-1)==(idx-3*(vesicle->vlist->n-2))%(vesicle->tape->nmono) + && idx<(3*vesicle->vlist->n-2+vesicle->tape->nmono*vesicle->tape->npoly+vesicle->tape->npoly)){ polyidx=(idx-3*(vesicle->vlist->n-2))/(vesicle->tape->nmono); //fprintf(stderr,"poly=%d, vertex=%d\n",polyidx,atoi(token[0])); vesicle->poly_list->poly[polyidx]->grafted_vtx=vesicle->vlist->vtx[atoi(token[0])]; diff --git a/src/tape b/src/tape index 620a4a3..12f88cd 100644 --- a/src/tape +++ b/src/tape @@ -1,6 +1,6 @@ ####### Vesicle definitions ########### # nshell is a number of divisions of dipyramid -nshell=10 +nshell=17 # dmax is the max. bond length (in units l_min) dmax=1.7 # dmin_interspecies in the min. dist. between different vertex species (in units l_min) @@ -25,7 +25,7 @@ ####### Polymer (brush) definitions ########### # npoly is a number of polymers attached to npoly distinct vertices on vesicle -npoly=0 +npoly=3 # nmono is a number of monomers in each polymer nmono=10 # Spring constant between monomers of the polymer @@ -33,7 +33,7 @@ ####### Filament (inside the vesicle) definitions ########### # nfil is a number of filaments inside the vesicle -nfil=0 +nfil=2 # nfono is a number of monomers in each filament nfono=300 # Persistence lenght of the filaments (in units l_min) @@ -54,7 +54,7 @@ ####### Program Control ############ #how many MC sweeps between subsequent records of states to disk #200000 -mcsweeps=2000 +mcsweeps=20 #how many initial mcsweeps*inititer MC sweeps before recording to disk? #2 inititer=0 diff --git a/test/Makefile.am b/test/Makefile.am deleted file mode 100644 index f8962fb..0000000 --- a/test/Makefile.am +++ /dev/null @@ -1,11 +0,0 @@ -doxygentestdir=../ -float3cmpdir=../ -confusetestdir=../ -codir=../ -doxygentest_PROGRAMS=doxygentest -doxygentest_SOURCES=doxygentest.c -float3cmp_PROGRAMS=float3cmp -float3cmp_SOURCES=float3cmp.c -confusetest_PROGRAMS=confusetest -confusetest_SOURCES=confusetest.c -confusetest_LDFLAGS=-lconfuse diff --git a/test/Ylmi2-2i.dat b/test/Ylmi2-2i.dat deleted file mode 100644 index dfee635..0000000 --- a/test/Ylmi2-2i.dat +++ /dev/null @@ -1,1448 +0,0 @@ - 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double precision co(10,21),pi - integer lmax,l,al, am, m - - pi=4.*datan(1.d0) - - lmax=10 - do 10 l=1,lmax - al=l - co(l,l+1)=dsqrt((2.*al+1.)/2./pi) - do 20 m=1,l-1 - am=m - co(l,l+1+m)=co(l,l+m)*dsqrt(1.d0/(al-am+1)/(al+am)) - co(l,l+1-m)=co(l,l+1+m) -20 continue - co(l,2*l+1)=co(l,2*l)*dsqrt(1.d0/(2.*al)) - co(l,1)=co(l,2*l+1) - co(l,l+1)=dsqrt((2.*al+1.)/4./pi) -10 continue - - do 30 l=1,lmax - do 40 m=1,2*l+1 - print *, 'co(',l,',',m,')=',co(l,m) -40 continue -30 continue - - end program cod - diff --git a/test/confusetest.c b/test/confusetest.c deleted file mode 100644 index 72d3377..0000000 --- a/test/confusetest.c +++ /dev/null @@ -1,34 +0,0 @@ - -#include <string.h> -#include "confuse.h" - -int main(void) -{ - - long int nshell=17,ncxmax=60, ncymax=60, nczmax=60; - double xk0=25.0, dmax=1.67,stepsize=0.15; - cfg_opt_t opts[] = { - CFG_SIMPLE_INT("nshell", &nshell), - CFG_SIMPLE_FLOAT("dmax", &dmax), - CFG_SIMPLE_FLOAT("xk0",&xk0), - CFG_SIMPLE_FLOAT("stepsize",&stepsize), - CFG_SIMPLE_INT("nxmax", &ncxmax), - CFG_SIMPLE_INT("nymax", &ncymax), - CFG_SIMPLE_INT("nzmax", &nczmax), - CFG_END() - }; - cfg_t *cfg; - int retval; - cfg = cfg_init(opts, 0); - retval=cfg_parse(cfg, "tape_new"); - - printf("nshell: %li\n", nshell); - printf("dmax: %f\n", dmax); - printf("xk0: %f\n", xk0); - printf("stepsize: %f\n", stepsize); - printf("nxmax: %li\n", ncxmax); - printf("nymax: %li\n", ncymax); - printf("nzmax: %li\n", nczmax); - return 0; -} - diff --git a/test/doxygentest.c b/test/doxygentest.c deleted file mode 100644 index ff6138f..0000000 --- a/test/doxygentest.c +++ /dev/null @@ -1,46 +0,0 @@ -/** @file doxygentest.c - @author Samo Penic - @date 4.3.2010 -*/ - -#include<stdio.h> - - -/** Defines the number of n/a items */ -#define N_A 10 - -/** @brief Structure that holds some info on three members - * - * This detailed description describes the structure more precisely. - * One member is also extra documented! - */ -typedef struct{ - int i; - char *a; /**< If you think you don't understand this, add a note to member -*/ - long *ptr; -} test; - -//typedef t_test test; - -/** @brief This is a dummy function to test doxygen documentation - * - * Some further explanation of the testfunction comes in the next lines - * when the brief has been satisfied. - * @param param1 is an integer - * @param param2 is a float - * @return function returns nothing - * - * TODO: Still not fully functional algorithm - */ -void testfunction(int param1, float param2){ - - - int i; /** This will add an extra line in the documentation block */ - - -} - -void main(){ - test i; -} diff --git a/test/float3cmp.c b/test/float3cmp.c deleted file mode 100644 index 0dadaff..0000000 --- a/test/float3cmp.c +++ /dev/null @@ -1,23 +0,0 @@ -#include<stdio.h> - -/** Compares positions of the vertices in two files to given accuracy - * - * @author Samo Penic - * @date to be done - * - * Usage: float3cmp vertexfile1 vertexfile2 eps - * - * Compares files with 3 floats in a line for similarities. Result of - * comparison is reported on stdout. -*/ -int main(int argv, char *argc[]){ - - if(argv!=4){ - fprintf(stderr,"Error. Usage: float3cmp vertexfile1 vertexfile2 eps\n"); - exit(1); - } - - fprintf("Comparing %s and %s for equality. Criterion: abs(float1-float2)< %f\n", argc[1], argc[2],argc[3]); - -return 0; -} diff --git a/test/parsecmdline.c b/test/parsecmdline.c deleted file mode 100644 index d15a8c8..0000000 --- a/test/parsecmdline.c +++ /dev/null @@ -1,40 +0,0 @@ -#include<stdio.h> -#include<stdlib.h> -#include<string.h> -int main(int argv, char *argc[]){ - - - char *commands, *backup, *saveptr, *saveopptr, *command, *operator[2], *operand; - int i,j; - if(argv!=2){ - fprintf(stderr, "Error. Usage: parsecmdline cmd1=1,cmd2=2,...\n"); - exit(1); - } - commands=(char *)malloc(10000*sizeof(char)); - backup=commands; - strcpy(commands,argc[1]); - - - - for(i=0; ;i++, commands=NULL){ - //breaks comma separated list of commands into specific commands. - command=strtok_r(commands,",",&saveptr); - if(command==NULL) break; - fprintf(stdout,"Command %d: %s\n",i,command); - //extracts name of command and value of command into operator[2] array. - for(j=0; j<2;j++,command=NULL){ - operator[j]=strtok_r(command,"=",&saveopptr); - if(operator[j]==NULL) break; - fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]); - } - //1. check: must have 2 operators. - if(j!=2) fprintf(stderr,"Error. Command no. %d is not formatted properly.\n",i); - //2. check: must be named properly. - //3. check: must be of right format (integer, double, string, ...) - - - } - - free(backup); - return 0; -} -- Gitblit v1.9.3