From aafd67f2d592799167864698ea07eb8aadcc86a7 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 25 May 2016 18:37:21 +0000
Subject: [PATCH] Merge branch 'master' of bitbucket.org:samop/trisurf-ng with work done on removing the memory leaks.
---
configure.ac | 3
src/snapshot.c | 2
python/tape | 2
python/trisurf/trisurf.py | 17 +++--
src/io.c | 3 +
src/tape | 16 +++--
python/MANIFEST.in | 1
Makefile.am | 2
src/initial_distribution.c | 4 +
src/general.h | 6 ++
build.sh | 7 +
src/vertexmove.c | 9 +++
/dev/null | 40 -------------
python/setup.py | 9 +++
python/trisurf/tsmgr.py | 8 ++
src/restore.c | 16 ++++-
16 files changed, 79 insertions(+), 66 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/aclocal.m4 b/aclocal.m4
deleted file mode 100644
index 7657505..0000000
--- a/aclocal.m4
+++ /dev/null
@@ -1,1364 +0,0 @@
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-[AC_ARG_ENABLE([silent-rules], [dnl
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-dnl A few 'make' implementations (e.g., NonStop OS and NextStep)
-dnl do not support nested variable expansions.
-dnl See automake bug#9928 and bug#10237.
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-
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 1a24bc2..a587e47 100755
--- a/build.sh
+++ b/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 ..
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/python/tape b/python/tape
index baaac60..f207db2 100644
--- a/python/tape
+++ b/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
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
index 310b4d3..8b36d27 100644
--- a/python/trisurf/trisurf.py
+++ b/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"))
diff --git a/python/trisurf/tsmgr.py b/python/trisurf/tsmgr.py
index adef0b2..fa7d20f 100644
--- a/python/trisurf/tsmgr.py
+++ b/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)
diff --git a/src/general.h b/src/general.h
index 547680e..dccee34 100644
--- a/src/general.h
+++ b/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;
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 4c82b35..ae7de0b 100644
--- a/src/initial_distribution.c
+++ b/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):
diff --git a/src/io.c b/src/io.c
index c35d42b..2461de5 100644
--- a/src/io.c
+++ b/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),
diff --git a/src/restore.c b/src/restore.c
index 643188b..14586c6 100644
--- a/src/restore.c
+++ b/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])];
diff --git a/src/snapshot.c b/src/snapshot.c
index 370ce4c..cabb1f8 100644
--- a/src/snapshot.c
+++ b/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){
diff --git a/src/tape b/src/tape
index baaac60..12f88cd 100644
--- a/src/tape
+++ b/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
diff --git a/src/vertexmove.c b/src/vertexmove.c
index b065cbb..4caa86f 100644
--- a/src/vertexmove.c
+++ b/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);
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 @@
- l, m, i (vertex id), Y_l^m(i)
- 2 -2 1 -0.0000000000000000 7.98716080604552755E-017 -4.23219779117647779E-016 10.724915113400144
- 2 -2 2 -5.53002604174509214E-003 7.98716080604552755E-017 1.0207810105846389 10.094037753788371
- 2 -2 3 4.47388504710780500E-003 0.97082043182687339 0.31543867980588625 10.094037753788371
- 2 -2 4 -1.70887202623525567E-003 0.60000002384185813 -0.82582918509820669 10.094037753788371
- 2 -2 5 -1.70887202623525437E-003 -0.60000002384185791 -0.82582918509820669 10.094037753788371
- 2 -2 6 4.47388504710780413E-003 -0.97082043182687316 0.31543867980588625 10.094037753788371
- 2 -2 7 -2.42944152525294901E-002 7.98716080604552755E-017 2.0415620211692782 9.4631603941765974
- 2 -2 8 -4.99032514569490004E-003 0.97082043182687339 1.3362196903905255 9.4631603941765974
- 2 -2 9 1.96545948076982877E-002 1.9416408636537466 0.63087735961177294 9.4631603941765974
- 2 -2 10 1.30648408463425389E-002 1.5708204556687313 -0.51039050529231988 9.4631603941765974
- 2 -2 11 -7.50738718143353911E-003 1.2000000476837160 -1.6516583701964129 9.4631603941765974
- 2 -2 12 -1.61490314012952621E-002 7.98716080604552755E-017 -1.6516583701964129 9.4631603941765974
- 2 -2 13 -7.50738718143353478E-003 -1.2000000476837160 -1.6516583701964129 9.4631603941765974
- 2 -2 14 1.30648408463425320E-002 -1.5708204556687313 -0.51039050529232011 9.4631603941765974
- 2 -2 15 1.96545948076982842E-002 -1.9416408636537466 0.63087735961177294 9.4631603941765974
- 2 -2 16 -4.99032514569490958E-003 -0.97082043182687316 1.3362196903905255 9.4631603941765974
- 2 -2 17 -5.86233602927273834E-002 7.98716080604552755E-017 3.0623430317539175 8.8322830345648242
- 2 -2 18 -2.98192585765955816E-002 0.97082043182687339 2.3570007009751648 8.8322830345648242
- 2 -2 19 6.73569351025355909E-003 1.9416408636537466 1.6516583701964120 8.8322830345648242
- 2 -2 20 4.74272947441819470E-002 2.9124612954806199 0.94631603941765952 8.8322830345648242
- 2 -2 21 4.15128803859999215E-002 2.5416408874956047 -0.19495182548643328 8.8322830345648242
- 2 -2 22 1.89206775392032553E-002 2.1708204795105894 -1.3362196903905261 8.8322830345648242
- 2 -2 23 -1.81156145978182519E-002 1.8000000715255742 -2.4774875552946192 8.8322830345648242
- 2 -2 24 -3.73499928588611405E-002 0.60000002384185824 -2.4774875552946192 8.8322830345648242
- 2 -2 25 -3.73499928588611613E-002 -0.60000002384185780 -2.4774875552946192 8.8322830345648242
- 2 -2 26 -1.81156145978182380E-002 -1.8000000715255742 -2.4774875552946192 8.8322830345648242
- 2 -2 27 1.89206775392032484E-002 -2.1708204795105894 -1.3362196903905263 8.8322830345648242
- 2 -2 28 4.15128803859999285E-002 -2.5416408874956047 -0.19495182548643350 8.8322830345648242
- 2 -2 29 4.74272947441819401E-002 -2.9124612954806199 0.94631603941765952 8.8322830345648242
- 2 -2 30 6.73569351025356863E-003 -1.9416408636537468 1.6516583701964123 8.8322830345648242
- 2 -2 31 -2.98192585765955885E-002 -0.97082043182687328 2.3570007009751648 8.8322830345648242
- 2 -2 32 -0.10850580591373692 7.98716080604552755E-017 4.0831240423385573 8.2014056749530511
- 2 -2 33 -7.18182499957342874E-002 0.97082043182687339 3.3777817115598041 8.2014056749530511
- 2 -2 34 -2.35627434133698146E-002 1.9416408636537466 2.6724393807810514 8.2014056749530511
- 2 -2 35 3.16516042562239447E-002 2.9124612954806199 1.9670970500022991 8.2014056749530511
- 2 -2 36 8.77830409725628424E-002 3.8832817273074931 1.2617547192235463 8.2014056749530511
- 2 -2 37 8.45527652494112852E-002 3.5124613193224778 0.12048685431945352 8.2014056749530511
- 2 -2 38 6.16880631243949124E-002 3.1416409113374626 -1.0207810105846393 8.2014056749530511
- 2 -2 39 2.06048785107032298E-002 2.7708205033524473 -2.1620488754887321 8.2014056749530511
- 2 -2 40 -3.35301380156943635E-002 2.4000000953674321 -3.3033167403928254 8.2014056749530511
- 2 -2 41 -6.49909980206040544E-002 1.2000000476837160 -3.3033167403928254 8.2014056749530511
- 2 -2 42 -7.62506394220501676E-002 7.98716080604552755E-017 -3.3033167403928254 8.2014056749530511
- 2 -2 43 -6.49909980206040683E-002 -1.2000000476837163 -3.3033167403928254 8.2014056749530511
- 2 -2 44 -3.35301380156943427E-002 -2.4000000953674321 -3.3033167403928254 8.2014056749530511
- 2 -2 45 2.06048785107032124E-002 -2.7708205033524473 -2.1620488754887326 8.2014056749530511
- 2 -2 46 6.16880631243949193E-002 -3.1416409113374626 -1.0207810105846398 8.2014056749530511
- 2 -2 47 8.45527652494112852E-002 -3.5124613193224778 0.12048685431945308 8.2014056749530511
- 2 -2 48 8.77830409725628286E-002 -3.8832817273074931 1.2617547192235463 8.2014056749530511
- 2 -2 49 3.16516042562239447E-002 -2.9124612954806199 1.9670970500022991 8.2014056749530511
- 2 -2 50 -2.35627434133698355E-002 -1.9416408636537466 2.6724393807810514 8.2014056749530511
- 2 -2 51 -7.18182499957343290E-002 -0.97082043182687305 3.3777817115598041 8.2014056749530511
- 2 -2 52 -0.17070406550548112 7.98716080604552755E-017 5.1039050529231966 7.5705283153412779
- 2 -2 53 -0.12955857874159454 0.97082043182687339 4.3985627221444439 7.5705283153412779
- 2 -2 54 -7.21557543473051732E-002 1.9416408636537466 3.6932203913656907 7.5705283153412779
- 2 -2 55 -3.25314015534867692E-003 2.9124612954806199 2.9878780605869379 7.5705283153412779
- 2 -2 56 6.94779033483622216E-002 3.8832817273074931 2.2825357298081852 7.5705283153412779
- 2 -2 57 0.13810249000282848 4.8541021591343663 1.5771933990294329 7.5705283153412779
- 2 -2 58 0.14015228058966739 4.4832817511493506 0.43592553412534008 7.5705283153412779
- 2 -2 59 0.12000360317317647 4.1124613431643358 -0.70534233077875275 7.5705283153412779
- 2 -2 60 7.74194456888264992E-002 3.7416409351793205 -1.8466101956828456 7.5705283153412779
- 2 -2 61 1.71409696568644125E-002 3.3708205271943052 -2.9878780605869384 7.5705283153412779
- 2 -2 62 -5.27504572500878607E-002 3.0000001192092900 -4.1291459254910308 7.5705283153412779
- 2 -2 63 -9.72125748532993994E-002 1.8000000715255740 -4.1291459254910308 7.5705283153412779
- 2 -2 64 -0.12201415435934908 0.60000002384185802 -4.1291459254910308 7.5705283153412779
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- 2 -2 66 -9.72125748532993161E-002 -1.8000000715255742 -4.1291459254910308 7.5705283153412779
- 2 -2 67 -5.27504572500878607E-002 -3.0000001192092900 -4.1291459254910308 7.5705283153412779
- 2 -2 68 1.71409696568644819E-002 -3.3708205271943052 -2.9878780605869384 7.5705283153412779
- 2 -2 69 7.74194456888264992E-002 -3.7416409351793205 -1.8466101956828456 7.5705283153412779
- 2 -2 70 0.12000360317317650 -4.1124613431643358 -0.70534233077875275 7.5705283153412779
- 2 -2 71 0.14015228058966739 -4.4832817511493506 0.43592553412534008 7.5705283153412779
- 2 -2 72 0.13810249000282848 -4.8541021591343663 1.5771933990294329 7.5705283153412779
- 2 -2 73 6.94779033483621383E-002 -3.8832817273074931 2.2825357298081856 7.5705283153412779
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- 2 -2 135 0.24835040339883210 -6.7957430227881135 2.2080707586412061 6.3087735961177280
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- 2 -2 152 0.32979719760020604 7.0249226386449557 0.24097370863890746 5.6778962365059549
- 2 -2 153 0.30707161244328574 6.6541022306599409 -0.90029415626518539 5.6778962365059549
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diff --git a/test/ampl.dat b/test/ampl.dat
deleted file mode 100644
index 3f12dfb..0000000
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- 16 1 -5.31259064517897173E-018
- 16 2 1.15243558828500029E-018
- 16 3 6.96057794735693847E-017
- 16 4 6.52709317829575803E-018
- 16 5 1.64553732588863730E-002
- 16 6 4.67244522234768496E-017
- 16 7 -4.57882850228523279E-018
- 16 8 -2.43800178350072628E-018
- 16 9 1.08058138580944904E-017
- 16 10 -4.99575981210059651E-018
- 16 11 -4.79518354637089915E-017
- 16 12 -4.89039396954734513E-017
- 16 13 -3.88449638414847413E-017
- 16 14 -1.02866646761716661E-016
- 16 15 1.64687523511047491E-002
- 16 16 2.33692997439192251E-017
- 17 -17 2.23435092087895029E-017
- 17 -16 2.08359055441275677E-017
- 17 -15 1.04561581319308839E-017
- 17 -14 -1.15460998226131598E-017
- 17 -13 2.22098327969865824E-017
- 17 -12 1.43960714705033021E-017
- 17 -11 4.81889515526975995E-019
- 17 -10 2.98773420007512284E-003
- 17 -9 8.85113307251360579E-018
- 17 -8 -6.09389797162940112E-017
- 17 -7 5.45710238926144459E-017
- 17 -6 1.87673913749583123E-017
- 17 -5 2.19229867515367745E-017
- 17 -4 -3.39965143709985984E-017
- 17 -3 1.60944535101798499E-017
- 17 -2 9.64939933512098946E-018
- 17 -1 1.07977914979258581E-017
- 17 0 8.80343934595941152E-002
- 17 1 -3.25260651745651330E-017
- 17 2 -8.04111282172575864E-019
- 17 3 4.69866116500905484E-017
- 17 4 -7.00369268935110791E-018
- 17 5 -6.25460368546631659E-003
- 17 6 4.04578676230580525E-017
- 17 7 1.02867519232604479E-017
- 17 8 -2.14754040292398383E-017
- 17 9 -3.47467687375478430E-017
- 17 10 1.87921799620084139E-017
- 17 11 -3.51481118904737374E-017
- 17 12 -3.61377601744820206E-018
- 17 13 -2.74699264719935881E-017
- 17 14 -5.56875757045907567E-017
- 17 15 5.84891495825615344E-003
- 17 16 -9.31086711199218013E-018
- 17 17 6.39471398870456753E-017
- 18 -18 -1.92319494135128462E-017
- 18 -17 -1.10036518540250102E-017
- 18 -16 3.98889032004373492E-018
- 18 -15 5.94697969373859012E-017
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- 18 -8 -5.35698195449612000E-017
- 18 -7 1.73457764089429587E-017
- 18 -6 1.25320642128641871E-017
- 18 -5 9.52819276214834388E-018
- 18 -4 -6.09863722023096244E-019
- 18 -3 2.13161511931944592E-017
- 18 -2 -6.50521303491302660E-019
- 18 -1 1.35069606305059795E-017
- 18 0 -1.98302791791529903E-002
- 18 1 -1.86482773667506763E-017
- 18 2 1.87064496217949721E-017
- 18 3 2.22532495902649785E-017
- 18 4 -1.01834659352394141E-017
- 18 5 -2.22635437500751029E-002
- 18 6 2.39499391830864164E-017
- 18 7 1.81745080165497046E-017
- 18 8 -1.52716173158212437E-017
- 18 9 -7.28825175378310606E-017
- 18 10 -1.14178170402092006E-017
- 18 11 -5.86715436136372505E-017
- 18 12 2.11530273461807450E-017
- 18 13 -2.74939733360699446E-017
- 18 14 2.93811683960907821E-017
- 18 15 -6.83782396515188190E-005
- 18 16 -3.67015794302638752E-017
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- 19 -7 -3.76123300979015292E-017
- 19 -6 1.04297284377790137E-017
- 19 -5 -1.60749762924649734E-017
- 19 -4 1.25902977279879202E-017
- 19 -3 8.56759060813532550E-018
- 19 -2 -2.62376925741492073E-017
- 19 -1 2.98922604451523163E-018
- 19 0 -7.31128664867429778E-002
- 19 1 -7.15573433840432926E-018
- 19 2 1.56655644151950064E-017
- 19 3 1.15196480826584846E-017
- 19 4 4.04866599130387656E-018
- 19 5 -1.89083746770740712E-003
- 19 6 1.32670219458387304E-017
- 19 7 1.23404230085479016E-017
- 19 8 -2.21048470607033187E-018
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- 19 18 3.58323561175770282E-017
- 19 19 3.19620327635968001E-018
- 20 -20 8.74637635650979579E-003
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- 20 -12 -2.56125259968594410E-017
- 20 -11 -4.71881246349572178E-017
- 20 -10 -3.30874988704420647E-003
- 20 -9 3.94093913966649094E-017
- 20 -8 2.39335975214949998E-017
- 20 -7 -5.64798618191930415E-017
- 20 -6 2.13507359849655215E-017
- 20 -5 -2.92946278623452819E-017
- 20 -4 -5.43456338958359098E-018
- 20 -3 1.40305540058870459E-018
- 20 -2 -4.61870125478824889E-017
- 20 -1 5.15703758114696720E-018
- 20 0 2.13355051465567054E-002
- 20 1 5.63785129692462306E-018
- 20 2 -4.23464880456753361E-018
- 20 3 -1.45554141656178970E-017
- 20 4 1.94195309069124896E-017
- 20 5 1.34256355764256988E-002
- 20 6 1.12176571505828150E-017
- 20 7 9.66416947213873632E-018
- 20 8 4.86038302073174971E-018
- 20 9 -5.11436053369339513E-018
- 20 10 -9.07713784318475419E-018
- 20 11 -3.16455742740290972E-017
- 20 12 -2.34478490669692635E-017
- 20 13 -4.34519365427563325E-017
- 20 14 -1.09001708260567617E-016
- 20 15 7.48792356690542327E-003
- 20 16 -2.46338826184015612E-018
- 20 17 -2.20895869461178960E-017
- 20 18 8.42717397771491549E-017
- 20 19 1.33835922623270314E-017
- 20 20 1.00353386423251370E-016
diff --git a/test/co.for b/test/co.for
deleted file mode 100644
index abce64d..0000000
--- a/test/co.for
+++ /dev/null
@@ -1,28 +0,0 @@
- program cod
- 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;
-}
--
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