Merge branch 'master' of bitbucket.org:samop/trisurf-ng

Samo Penic

2016-05-24 3f5658c8e3ac0b1febafe06c81c334f9b31a73be

Merge branch 'master' of bitbucket.org:samop/trisurf-ng

 Makefile.am

@@ -1 +1 @@
SUBDIRS=test src
SUBDIRS=src

 bin/trisurf-deploy

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 build.sh

@@ -8,4 +8,6 @@
make clean
make
sudo make install

cd python
sudo python3 setup.py install
cd ..

 configure.ac

@@ -51,6 +51,5 @@
AC_CHECK_FUNCS([pow sqrt strndup])

AC_CONFIG_FILES([Makefile
                 src/Makefile
                 test/Makefile])
                 src/Makefile])
AC_OUTPUT

 python/MANIFEST.in

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@@ -0,0 +1 @@
recursive-include trisurf *.py

 python/setup.py

New file
@@ -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"]
)

 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])];

 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

 test/Makefile.am

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 test/Ylmi2-2i.dat

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 test/ampl.dat

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 test/co.for

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 test/confusetest.c

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 test/doxygentest.c

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 test/float3cmp.c

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 test/parsecmdline.c

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