Merge branch 'master' of bitbucket.org:samop/trisurf-ng with work done on r...

Samo Penic

2016-05-25 aafd67f2d592799167864698ea07eb8aadcc86a7

Merge branch 'master' of bitbucket.org:samop/trisurf-ng with work done on removing the memory leaks.

Conflicts:
	aclocal.m4

 Makefile.am

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

 aclocal.m4

File was deleted

 bin/trisurf-deploy

File was deleted

 build.sh

@@ -5,6 +5,9 @@
automake -ac
autoconf
./configure
make clean
make
make install

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

New file
@@ -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"]
)

 python/tape

@@ -52,7 +52,7 @@
####### Program Control ############
#how many MC sweeps between subsequent records of states to disk
#200000
mcsweeps=20
mcsweeps=200
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
#2
inititer=0

 python/trisurf/trisurf.py

@@ -1,5 +1,3 @@
#!/usr/bin/python3

import configobj
import xml.etree.ElementTree as ET
import base64
@@ -84,6 +82,9 @@
        '''
        try:
            self.config=configobj.ConfigObj(tape)
            with open (tape, "r") as myfile:
                self.rawText=myfile.read() #read the file

        except:
            print("Error reading or parsing tape file!\n")
            exit(1)
@@ -91,6 +92,7 @@
    def setTape(self, string):
        '''Method setTape(string) parses the string in memory that hold the tape contents.'''
        self.config=configobj.ConfigObj(io.StringIO(string))
        self.rawText=string
        return

    def getValue(self,key):
@@ -364,8 +366,8 @@
                else:
                    try:
                        with open (os.path.join(self.Dir.fullpath(),"tape"), "w") as myfile:
                            myfile.write("#This is automatically generated tape file from snapshot")
                            myfile.write(str(self.tape))
                            #myfile.write("#This is automatically generated tape file from snapshot")
                            myfile.write(str(self.tape.rawText))
                    except:
                        print("Error -- cannot make tapefile  "+ os.path.join(self.Dir.fullpath(),"tape")+" from the snapshot in the running directory")
                        exit(1)
@@ -395,8 +397,6 @@
            print("Process in "+self.Dir.fullpath()+" already running. Not starting.")
        return

    def stop(self):
        pass

    def setMaindir(self,prefix,variables):
        maindir=""
@@ -441,6 +441,11 @@
            report=["N/A","N/A",statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
        return report


    def stop(self):
        p=psutil.Process(self.getPID())
        p.kill()

    def writeComment(self, data, mode='w'):
        self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
        self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment"))

 python/trisurf/tsmgr.py

@@ -1,6 +1,7 @@
import sys, getopt
import tabulate
import subprocess,re
import psutil

def printHelp():
    print('Python module tsmgr accept following switches:\n')
@@ -9,6 +10,7 @@
    print('[-R]               : raw output for -s switch');
    print('[-r]               : run process');
    print('[-s]               : process status');
    print('[-k]               : kill process');
    print('[-c comment text]  : write new comment for process');
    print('[-a comment text]  : append additional comment for process');
    print('[-h]               : print help');
@@ -29,7 +31,7 @@
    processno=0
    raw=False
    try:
        opts, args = getopt.getopt(argv,"Ra:n:hrsc:")
        opts, args = getopt.getopt(argv,"Ra:n:hrskc:")
    except getopt.GetoptError:
        printHelp()
        sys.exit(2)
@@ -76,7 +78,9 @@
            if processno:
                Runs[processno-1].writeComment("\n"+arg, 'a')

			
        elif opt == '-k':
            if processno:
                Runs[processno-1].stop()
        else:
            printHelp()
            sys.exit(2)

 src/general.h

@@ -260,6 +260,9 @@
    long int nfil;
    long int nfono;
    long int R_nucleus;
    ts_double R_nucleusX;
    ts_double R_nucleusY;
    ts_double R_nucleusZ;
    long int pswitch;
    long int constvolswitch;
    long int constareaswitch;
@@ -307,6 +310,9 @@
    ts_int pswitch;
    ts_tape *tape;
    ts_double R_nucleus;
    ts_double R_nucleusX;
    ts_double R_nucleusY;
    ts_double R_nucleusZ;
    ts_double area;
} ts_vesicle;


 src/initial_distribution.c

@@ -52,7 +52,9 @@
    ts_vertex *vtx;
    ts_tape *tape=vesicle->tape;
    vesicle->R_nucleus=tape->R_nucleus*tape->R_nucleus;

    vesicle->R_nucleusX=tape->R_nucleusX*tape->R_nucleusX;
    vesicle->R_nucleusY=tape->R_nucleusY*tape->R_nucleusY;
    vesicle->R_nucleusZ=tape->R_nucleusZ*tape->R_nucleusZ;
    vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;

    //Initialize grafted polymers (brush):

 src/io.c

@@ -1031,6 +1031,9 @@
    CFG_SIMPLE_INT("nfil",&tape->nfil),
    CFG_SIMPLE_INT("nfono",&tape->nfono),
    CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
    CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
    CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
    CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
    CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
    CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
        CFG_SIMPLE_FLOAT("xk0",&tape->xk0),

 src/restore.c

@@ -57,6 +57,7 @@
                        if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Points"))){
                            //fprintf(stderr,"Found point data\n");
                            if(vesicle!=NULL)
                                //fprintf(stderr,"Fils: %ld, Nfono: %ld\n", vesicle->tape->nfil, vesicle->tape->nfono);
                                parseXMLVertexPosition(vesicle, doc, cur2);
                        }
                        if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Cells"))){
@@ -286,7 +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"))){
@@ -301,12 +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");
@@ -316,6 +324,7 @@
        }
        child=child->next;
    }
    //fprintf(stderr,"Came here\n");
    //fprintf(stderr,"Vertices position j=%d\n",idx);    

    return TS_SUCCESS;
@@ -340,7 +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/snapshot.c

@@ -57,7 +57,7 @@
    fprintf(fh, "<trisurfversion>Trisurf (commit %s), compiled on %s %s</trisurfversion>\n",TS_VERSION, __DATE__,  __TIME__);
    fprintf(fh, "<dumpdate>%s</dumpdate>\n", c_time_string);

    fprintf(fh, "<tape>\n");
    fprintf(fh, "<tape>");
        fprintf(fh,"%s",tapetxt);    
    fprintf(fh, "</tape>\n");
    if(vesicle->poly_list!=NULL){

 src/tape

@@ -1,6 +1,6 @@
####### Vesicle definitions ###########
# nshell is a number of divisions of dipyramid
nshell=5
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)
@@ -12,12 +12,12 @@

# Pressure calculations
# (pswitch=1: calc. p*dV energy contribution)
pswitch = 0
pswitch = 1
# pressure difference: p_inside - p_outside (in units kT/l_min^3):
pressure=0.0
pressure=-10.0

#Constant volume constraint (0 disable constant volume, 1 enable wiht additional vertex move, 2 enable with epsvol)
constvolswitch=2
constvolswitch=0
constvolprecision=1e-14

#Constant area constraint (0 disable constant area, 2 enable constant area with epsarea)
@@ -25,7 +25,7 @@

####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
npoly=2
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)
@@ -42,7 +42,9 @@
####### Nucleus (inside the vesicle) ###########
# Radius of an impenetrable hard sphere inside the vesicle
R_nucleus=0

R_nucleusX=2.0
R_nucleusY=6.0
R_nucleusZ=2.0
#######  Cell definitions ############
nxmax=60
nymax=60

 src/vertexmove.c

@@ -72,10 +72,19 @@

// TODO: Maybe faster if checks only nucleus-neighboring cells
// Nucleus penetration check:
if(vesicle->R_nucleus>0.0){
    if (vtx->x*vtx->x + vtx->y*vtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
        vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
        return TS_FAIL;
    }
} else if(vesicle->R_nucleusX>0.0){
//    fprintf(stderr,"DEBUG, (Rx, Ry,Rz)^2=(%f,%f,%f)\n",vesicle->R_nucleusX, vesicle->R_nucleusY, vesicle->R_nucleusZ);
    if ((vtx->x*vtx->x)/vesicle->R_nucleusX + vtx->y*vtx->y/vesicle->R_nucleusY + (vtx->z*vtx->z)/vesicle->R_nucleusZ < 1.0){
        vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
        return TS_FAIL;
    }

}

//self avoidance check with distant vertices
    cellidx=vertex_self_avoidance(vesicle, vtx);

 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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