From 60c2b879f26c5f008af0df7d7f159d33077225ac Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 09 Mar 2019 19:47:16 +0000
Subject: [PATCH] Cleanup of stretching energy plugin
---
src/plugins.c | 158 ++++++++++++++++++++++++++++++++++++++++++++++------
1 files changed, 138 insertions(+), 20 deletions(-)
diff --git a/src/plugins.c b/src/plugins.c
index 7681984..3146c2a 100644
--- a/src/plugins.c
+++ b/src/plugins.c
@@ -1,28 +1,91 @@
/* This is a first attempt in implementation of plugins to Trisurf-ng. */
/*
-1. Capabilities of Plugin
--------------------------
-Every plugin should list it's capabilities -- that is what subrutines are available in it. Capabilities list for the moment are:
+Options for tape:
-* PLUGIN_PROGRAM_START (requires subrutine void at_start(void)): runs at startup
-* PLUGIN_VESICLE_INITIALIZED (requires subrutine void after_vesicle_init(vesicle *vesicle):
- runs after vesicle gets initialized.
+extra_plugin_path = "..." (OPTIONAL)
-* PLUGIN_VERTEX_MOVE (requires subrutines:
+vesicle bipyramid {
+ nshell=23
+}
- ts_bool vm_hard_constraint(vesicle *vesicle, vtx *vtx, vtx *old_vtx)
- ts_double vm_energy_before(vesicle *vesicle, vtx *vtx)
- ts_double vm_energy_after(vesicle *vesicle, vtx *vtx)
- ts_double vm_new_state_accepted(vesicle *vesicle, vtx *vtx)
- ts_double vm_new_state_rejected(vesicle *vesicle, vtx *vtx)
+vesicle vtufile {
+ filename="filename"
+}
- )
+vesicle vtudatabase {
+ run_id=123
+ timestep=999
+}
- these subrutines are added into the vertex move into right places
+vesicle properties {
+ xk0=20
+ dmax=1.7
+ dmin_interspecies=1.2
+ stepsize=0.15
+}
-* PLUGIN_BOND_FLIP ( N/A yet)
+space properties {
+ nxmax=60
+ nymax=60
+ nzmax=60
+}
+
+loop control {
+ inner=1000
+ outer=1000
+}
+
+plugin pressure {
+ pressure=10
+}
+
+plugin constant_volume {
+ precision=1e14
+}
+
+plugin constant_area {
+
+}
+
+plugin confinement_plate {
+ distance=5
+ force=10
+ coordinate=2 // 0=x,1=y,2=z
+}
+
+plugin spherical_harmonics {
+ lmax=21
+ filename="abc.csv"
+}
+
+plugin spontaneous_curvature {
+ c0=2
+ N=100
+ w=10
+ force=3
+}
+
+plugin filament {
+ monomers=100
+ xi=10
+}
+
+plugin polymer {
+ polymers = 100
+ monomers = 10
+ elastic_coefficient=100
+ is_internal = true
+}
+
+plugin nucleus {
+ R_nucleus=10
+ R_nucleusX=0
+ R_nucleusY=0
+ R_nucleusZ=0
+}
+
*/
#include "plugins.h"
#include <stdlib.h>
@@ -32,14 +95,18 @@
ts_plugin *init_plugin(ts_char *filename){
ts_plugin *plugin = (ts_plugin *)calloc(1, sizeof(ts_plugin));
- plugin->filename=(ts_char *)calloc(strlen(filename),sizeof(ts_char));
+ plugin->filename=(ts_char *)calloc(strlen(filename)+1,sizeof(ts_char));
strcpy(plugin->filename,filename);
plugin->libhandle = dlopen(plugin->filename, RTLD_NOW);
if(!plugin->libhandle){
- ts_fprintf(stderr,"Error loading plugin: %s\n", filename);
+ ts_fprintf(stderr,"Error loading plugin: %s\n", plugin->filename);
fatal("Exiting",235);
}
ts_plugin_details* (*get_plugin_details)(void) = dlsym(plugin->libhandle, "init");
+ if(get_plugin_details==NULL){
+ ts_fprintf(stderr,"Plugin %s invalid. No init() function.\n", plugin->filename);
+ fatal("Exiting", 236);
+ }
plugin->details = get_plugin_details();
plugin->function = (ts_plugin_function *)calloc(1,sizeof(ts_plugin_function));
@@ -47,8 +114,11 @@
plugin->function->at_start = dlsym(plugin->libhandle, "at_start");
plugin->function->after_vesicle_init = dlsym(plugin->libhandle, "after_vesicle_init");
plugin->function->vm_hard_constraint = dlsym(plugin->libhandle, "vm_hard_constraint");
- plugin->function->vm_energy_before = dlsym(plugin->libhandle, "vm_energy_before");
- plugin->function->vm_energy_after = dlsym(plugin->libhandle, "vm_energy_after");
+ plugin->function->vm_energy_before_prepare = dlsym(plugin->libhandle, "vm_energy_before_prepare");
+ plugin->function->vm_energy_before_execute = dlsym(plugin->libhandle, "vm_energy_before_execute");
+ plugin->function->vm_energy_after_prepare = dlsym(plugin->libhandle, "vm_energy_after_prepare");
+ plugin->function->vm_energy_after_execute = dlsym(plugin->libhandle, "vm_energy_after_execute");
+ plugin->function->vm_before_montecarlo_constraint = dlsym(plugin->libhandle, "vm_before_montecarlo_constraint");
plugin->function->vm_new_state_rejected = dlsym(plugin->libhandle, "vm_new_state_rejected");
plugin->function->vm_new_state_accepted = dlsym(plugin->libhandle, "vm_new_state_accepted");
@@ -56,12 +126,59 @@
}
+ts_plugin_chain *plugin_to_chain(ts_plugin_chain *chain, ts_plugin *plugin){
+ ts_plugin_chain *retchain;
+ if(chain!=NULL){
+ retchain=chain;
+ while(chain->next!=NULL){
+ chain=chain->next;
+ }
+ chain->next=(ts_plugin_chain *)calloc(1,sizeof(ts_plugin_chain));
+ chain->next->plugin=plugin;
+ return retchain;
+ } else {
+ chain=(ts_plugin_chain *)calloc(1,sizeof(ts_plugin_chain));
+ chain->plugin=plugin;
+ return chain;
+ }
+}
+
+
ts_plugin_list *init_plugin_list(ts_char **plugin_filenames, ts_uint number_of_plugins){
ts_plugin_list *plist=(ts_plugin_list *)calloc(1, sizeof(ts_plugin_list));
plist->plugin=(ts_plugin **)calloc(number_of_plugins, sizeof(ts_plugin *));
+ plist->chain=(ts_plugin_chains *)calloc(1, sizeof(ts_plugin_chains));
for(int i=0;i<number_of_plugins;i++){
plist->plugin[i]=init_plugin(plugin_filenames[i]);
+ if(plist->plugin[i]->function->cleanup!=NULL){
+ plist->chain->cleanup=plugin_to_chain(plist->chain->cleanup, plist->plugin[i]);
+ }
+ 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->after_vesicle_init!=NULL){
+ plist->chain->after_vesicle_init=plugin_to_chain(plist->chain->after_vesicle_init, 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]);
+ }
+ if(plist->plugin[i]->function->vm_before_montecarlo_constraint!=NULL){
+ plist->chain->vm_before_montecarlo_constraint=plugin_to_chain(plist->chain->vm_before_montecarlo_constraint, plist->plugin[i]);
+ }
+ if(plist->plugin[i]->function->vm_new_state_accepted!=NULL){
+ plist->chain->vm_new_state_accepted=plugin_to_chain(plist->chain->vm_new_state_accepted, plist->plugin[i]);
+ }
+ if(plist->plugin[i]->function->vm_new_state_rejected!=NULL){
+ plist->chain->vm_new_state_rejected=plugin_to_chain(plist->chain->vm_new_state_rejected, plist->plugin[i]);
+ }
}
+ plist->n=number_of_plugins;
return plist;
}
@@ -74,9 +191,10 @@
free(plugin);
}
-void free_plugin_list(ts_plugin_list *plist){
+void plugin_list_free(ts_plugin_list *plist){
for(int i=0;i<plist->n;i++){
free_plugin(plist->plugin[i]);
}
+ free(plist->chain);
free(plist);
}
--
Gitblit v1.9.3