Some changes to plugins to allow storage of data. Pressure is a plugin now

Samo Penic

2019-02-28 36dba86649e71d2a56657320ddf98a1af2055023

Some changes to plugins to allow storage of data. Pressure is a plugin now

 src/general.h

@@ -309,7 +309,7 @@
    void (*at_start)(int argc, char **argv);
    void *(*after_vesicle_init)(void *vesicle);
    ts_bool (*vm_hard_constraint)(void *vesicle, ts_vertex *vtx, ts_vertex *odl_vtx);
    ts_double (*vm_energy_before_prepare)(void *vesicle, ts_vertex *vtx);
    void (*vm_energy_before_prepare)(void *vesicle, ts_vertex *vtx);
    ts_double (*vm_energy_before_execute)(void *vesicle, ts_vertex *vtx);
    ts_double (*vm_energy_after_prepare)(void *vesicle, ts_vertex *vtx);
    ts_double (*vm_energy_after_execute)(void *vesicle, ts_vertex *vtx);
@@ -322,6 +322,7 @@
    ts_char *name;
    ts_char *description;
    ts_char *author;
    void *data;
} ts_plugin_details;

typedef struct {
@@ -341,6 +342,8 @@
    ts_plugin_chain *at_start;
    ts_plugin_chain *after_vesicle_init;
    ts_plugin_chain *vm_hard_constraint;
    ts_plugin_chain *vm_energy_before_prepare;
    ts_plugin_chain *vm_energy_after_execute;
    ts_plugin_chain *cleanup;
} ts_plugin_chains;

@@ -349,6 +352,7 @@
    ts_uint n;
    ts_plugin **plugin;
    ts_plugin_chains *chain;
    ts_plugin_chain *pointer;
} ts_plugin_list;

/* end plugins */

 src/main.c

@@ -29,14 +29,17 @@
    ts_char *plugin0 = (ts_char *)calloc(255,sizeof(ts_char));
    ts_char *plugin1 = (ts_char *)calloc(255,sizeof(ts_char));
    ts_char *plugin2 = (ts_char *)calloc(255,sizeof(ts_char));
    ts_char *plugin3 = (ts_char *)calloc(255,sizeof(ts_char));
    strcpy(plugin0,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/demoplugin.so");
    strcpy(plugin1,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/vmdefaulthardconstraints.so");
    strcpy(plugin2,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/plane_confinement.so");
    ts_char **plugins=(ts_char **)calloc(3,sizeof(ts_char *));
    strcpy(plugin3,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/pressure.so");
    ts_char **plugins=(ts_char **)calloc(4,sizeof(ts_char *));
    *plugins=plugin0;
    plugins[1]=plugin1;
    plugins[2]=plugin2;
    ts_plugin_list *plist=init_plugin_list(plugins,3);
    plugins[3]=plugin3;
    ts_plugin_list *plist=init_plugin_list(plugins,4);
    //printf("%s", plist->chain->at_start->next->plugin->filename);
    //ts_fprintf(stdout, "TRISURF in PRVI PLUGIN %s\n", plist->plugin[0]->details->name);
    ts_vesicle *vesicle;

 src/plugins.c

@@ -155,9 +155,17 @@
        if(plist->plugin[i]->function->at_start!=NULL){
            plist->chain->at_start=plugin_to_chain(plist->chain->at_start, plist->plugin[i]);
        }
        if(plist->plugin[i]->function->vm_hard_constraint!=NULL){
            plist->chain->vm_hard_constraint=plugin_to_chain(plist->chain->vm_hard_constraint, plist->plugin[i]);
        }
        if(plist->plugin[i]->function->vm_energy_before_prepare!=NULL){
            plist->chain->vm_energy_before_prepare=plugin_to_chain(plist->chain->vm_energy_before_prepare, plist->plugin[i]);
        }
        if(plist->plugin[i]->function->vm_energy_after_execute!=NULL){
            plist->chain->vm_energy_after_execute=plugin_to_chain(plist->chain->vm_energy_after_execute, plist->plugin[i]);
        }

    }
    //printf("%s", plist->chain->at_start->next->plugin->filename);
    plist->n=number_of_plugins;
    return plist;
}    

 src/plugins/.libs/demo_plugin.o

Binary files differ

 src/plugins/.libs/demoplugin.a

Binary files differ

 src/plugins/.libs/demoplugin.so

Binary files differ

 src/plugins/Makefile

@@ -150,6 +150,12 @@
    $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
    $(AM_CFLAGS) $(CFLAGS) $(plane_confinement_la_LDFLAGS) \
    $(LDFLAGS) -o $@
pressure_la_LIBADD =
am_pressure_la_OBJECTS = pressure.lo
pressure_la_OBJECTS = $(am_pressure_la_OBJECTS)
pressure_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
    $(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
    $(pressure_la_LDFLAGS) $(LDFLAGS) -o $@
vmdefaulthardconstraints_la_LIBADD =
am_vmdefaulthardconstraints_la_OBJECTS = default_hard_constraints.lo
vmdefaulthardconstraints_la_OBJECTS =  \
@@ -193,10 +199,10 @@
am__v_CCLD_0 = @echo "  CCLD    " $@;
am__v_CCLD_1 = 
SOURCES = $(demoplugin_la_SOURCES) $(nucleus_la_SOURCES) \
    $(plane_confinement_la_SOURCES) \
    $(plane_confinement_la_SOURCES) $(pressure_la_SOURCES) \
    $(vmdefaulthardconstraints_la_SOURCES)
DIST_SOURCES = $(demoplugin_la_SOURCES) $(nucleus_la_SOURCES) \
    $(plane_confinement_la_SOURCES) \
    $(plane_confinement_la_SOURCES) $(pressure_la_SOURCES) \
    $(vmdefaulthardconstraints_la_SOURCES)
am__can_run_installinfo = \
  case $$AM_UPDATE_INFO_DIR in \
@@ -346,7 +352,7 @@
top_builddir = ../..
top_srcdir = ../..
AM_CFLAGS = -Wall -Werror -DTS_VERSION=\"$(GITVERSION)\" -fgnu89-inline -Wno-error=date-time -I..
lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la
lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la
demoplugin_la_SOURCES = demo_plugin.c
demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic
vmdefaulthardconstraints_la_SOURCES = default_hard_constraints.c
@@ -355,6 +361,8 @@
nucleus_la_LDFLAGS = -module -avoid-version -export-dynamic
plane_confinement_la_SOURCES = plane_confinement.c 
plane_confinement_la_LDFLAGS = -module -avoid-version -export-dynamic
pressure_la_SOURCES = pressure.c 
pressure_la_LDFLAGS = -module -avoid-version -export-dynamic
all: all-am

.SUFFIXES:
@@ -433,6 +441,9 @@
plane_confinement.la: $(plane_confinement_la_OBJECTS) $(plane_confinement_la_DEPENDENCIES) $(EXTRA_plane_confinement_la_DEPENDENCIES) 
    $(AM_V_CCLD)$(plane_confinement_la_LINK) -rpath $(libdir) $(plane_confinement_la_OBJECTS) $(plane_confinement_la_LIBADD) $(LIBS)

pressure.la: $(pressure_la_OBJECTS) $(pressure_la_DEPENDENCIES) $(EXTRA_pressure_la_DEPENDENCIES) 
    $(AM_V_CCLD)$(pressure_la_LINK) -rpath $(libdir) $(pressure_la_OBJECTS) $(pressure_la_LIBADD) $(LIBS)

vmdefaulthardconstraints.la: $(vmdefaulthardconstraints_la_OBJECTS) $(vmdefaulthardconstraints_la_DEPENDENCIES) $(EXTRA_vmdefaulthardconstraints_la_DEPENDENCIES) 
    $(AM_V_CCLD)$(vmdefaulthardconstraints_la_LINK) -rpath $(libdir) $(vmdefaulthardconstraints_la_OBJECTS) $(vmdefaulthardconstraints_la_LIBADD) $(LIBS)

@@ -446,6 +457,7 @@
include ./$(DEPDIR)/demo_plugin.Plo
include ./$(DEPDIR)/nucleus.Plo
include ./$(DEPDIR)/plane_confinement.Plo
include ./$(DEPDIR)/pressure.Plo

.c.o:
    $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<

 src/plugins/Makefile.am

@@ -1,5 +1,5 @@
AM_CFLAGS = -Wall -Werror -DTS_VERSION=\"$(GITVERSION)\" -fgnu89-inline -Wno-error=date-time -I..
lib_LTLIBRARIES= demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la
lib_LTLIBRARIES= demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la
demoplugin_la_SOURCES= demo_plugin.c
demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic

@@ -12,3 +12,6 @@
plane_confinement_la_SOURCES = plane_confinement.c 
plane_confinement_la_LDFLAGS = -module -avoid-version -export-dynamic

pressure_la_SOURCES = pressure.c 
pressure_la_LDFLAGS = -module -avoid-version -export-dynamic


 src/plugins/Makefile.in

@@ -150,6 +150,12 @@
    $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
    $(AM_CFLAGS) $(CFLAGS) $(plane_confinement_la_LDFLAGS) \
    $(LDFLAGS) -o $@
pressure_la_LIBADD =
am_pressure_la_OBJECTS = pressure.lo
pressure_la_OBJECTS = $(am_pressure_la_OBJECTS)
pressure_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
    $(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
    $(pressure_la_LDFLAGS) $(LDFLAGS) -o $@
vmdefaulthardconstraints_la_LIBADD =
am_vmdefaulthardconstraints_la_OBJECTS = default_hard_constraints.lo
vmdefaulthardconstraints_la_OBJECTS =  \
@@ -193,10 +199,10 @@
am__v_CCLD_0 = @echo "  CCLD    " $@;
am__v_CCLD_1 = 
SOURCES = $(demoplugin_la_SOURCES) $(nucleus_la_SOURCES) \
    $(plane_confinement_la_SOURCES) \
    $(plane_confinement_la_SOURCES) $(pressure_la_SOURCES) \
    $(vmdefaulthardconstraints_la_SOURCES)
DIST_SOURCES = $(demoplugin_la_SOURCES) $(nucleus_la_SOURCES) \
    $(plane_confinement_la_SOURCES) \
    $(plane_confinement_la_SOURCES) $(pressure_la_SOURCES) \
    $(vmdefaulthardconstraints_la_SOURCES)
am__can_run_installinfo = \
  case $$AM_UPDATE_INFO_DIR in \
@@ -346,7 +352,7 @@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
AM_CFLAGS = -Wall -Werror -DTS_VERSION=\"$(GITVERSION)\" -fgnu89-inline -Wno-error=date-time -I..
lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la
lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la
demoplugin_la_SOURCES = demo_plugin.c
demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic
vmdefaulthardconstraints_la_SOURCES = default_hard_constraints.c
@@ -355,6 +361,8 @@
nucleus_la_LDFLAGS = -module -avoid-version -export-dynamic
plane_confinement_la_SOURCES = plane_confinement.c 
plane_confinement_la_LDFLAGS = -module -avoid-version -export-dynamic
pressure_la_SOURCES = pressure.c 
pressure_la_LDFLAGS = -module -avoid-version -export-dynamic
all: all-am

.SUFFIXES:
@@ -433,6 +441,9 @@
plane_confinement.la: $(plane_confinement_la_OBJECTS) $(plane_confinement_la_DEPENDENCIES) $(EXTRA_plane_confinement_la_DEPENDENCIES) 
    $(AM_V_CCLD)$(plane_confinement_la_LINK) -rpath $(libdir) $(plane_confinement_la_OBJECTS) $(plane_confinement_la_LIBADD) $(LIBS)

pressure.la: $(pressure_la_OBJECTS) $(pressure_la_DEPENDENCIES) $(EXTRA_pressure_la_DEPENDENCIES) 
    $(AM_V_CCLD)$(pressure_la_LINK) -rpath $(libdir) $(pressure_la_OBJECTS) $(pressure_la_LIBADD) $(LIBS)

vmdefaulthardconstraints.la: $(vmdefaulthardconstraints_la_OBJECTS) $(vmdefaulthardconstraints_la_DEPENDENCIES) $(EXTRA_vmdefaulthardconstraints_la_DEPENDENCIES) 
    $(AM_V_CCLD)$(vmdefaulthardconstraints_la_LINK) -rpath $(libdir) $(vmdefaulthardconstraints_la_OBJECTS) $(vmdefaulthardconstraints_la_LIBADD) $(LIBS)

@@ -446,6 +457,7 @@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/demo_plugin.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/nucleus.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/plane_confinement.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pressure.Plo@am__quote@

.c.o:
@am__fastdepCC_TRUE@    $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<

 src/plugins/demo_plugin.o

Binary files differ

 src/plugins/pressure.c

New file
@@ -0,0 +1,37 @@
#include <stdlib.h>
#include "general.h"
#include "vertex.h"
#include "cell.h"
char plugin_name[] = "Pressure";
char plugin_description[]= "Defines extra energy term for relative pressure difference between the inner vesicle and outer vesicle";
char plugin_author[] = "SAMO PENIC";

ts_plugin_details *init (){
    ts_plugin_details *details=(ts_plugin_details *)calloc(1,sizeof(ts_plugin_details));
    details->name = plugin_name;
    details->data = (void *)calloc(1,sizeof(ts_double));
    return details;	
}

void vm_energy_before_prepare(ts_vesicle *vesicle, ts_vertex *vtx){
    if(vesicle->pswitch == 1){
    ts_double *dvol=(ts_double *)vesicle->plist->pointer->plugin->details->data;
    ts_uint i;
    //printf ("DVOL was %f\n", *dvol);
    *dvol=0;
    for(i=0;i<vtx->tristar_no;i++) *dvol-=vtx->tristar[i]->volume;
    //printf ("DVOL is %f\n", *dvol);

    }
}

ts_double vm_energy_after_execute(ts_vesicle *vesicle, ts_vertex *vtx){
    ts_double delta_energy=0;
    if(vesicle->pswitch == 1){
        ts_double *dvol=(ts_double *)vesicle->plist->pointer->plugin->details->data;
        ts_uint i;
        for(i=0;i<vtx->tristar_no;i++) *dvol+=vtx->tristar[i]->volume;
        delta_energy=-vesicle->pressure*(*dvol);
    }
    return delta_energy;
}

 src/vertexmove.c

@@ -35,13 +35,6 @@
    vtx->y=vtx->y+r*sintheta*sin(phi);
    vtx->z=vtx->z+r*costheta;

// plane confinement check whether the new position of vertex will be out of bounds
    if(vesicle->tape->plane_confinement_switch){
        if(vtx->z>vesicle->confinement_plane.z_max || vtx->z<vesicle->confinement_plane.z_min){
        vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
        return TS_FAIL;
        }
    }

/* Entry point for plugin vm_hard_constraint() function */
    ts_plugin_chain *ptr=vesicle->plist->chain->vm_hard_constraint;
@@ -53,14 +46,21 @@
        }
        ptr=ptr->next;
    }
/* End of vm_hard_constraint() */


 
//if all the tests are successful, then energy for vtx and neighbours is calculated
/* Backuping the neighbours */ 
    for(i=0;i<vtx->neigh_no;i++){
    memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
    }

/* Entry point for plugin vm_energy_before_prepare() */

    vesicle->plist->pointer=vesicle->plist->chain->vm_energy_before_prepare;
    while(vesicle->plist->pointer!=NULL){
        vesicle->plist->pointer->plugin->function->vm_energy_before_prepare(vesicle, vtx);
        vesicle->plist->pointer=vesicle->plist->pointer->next;
    }
/* Calculate energy for vtx and neighbours */
    if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch>0){
        for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
    }