int main(int argc, char *argv[]) {
struct adjlog tg;
struct opts opts;
int optind;
TemporalGraphLog tgl;
optind = readopts(argc, argv, &opts);
INFO("Loading graph...");
//read_stdin(&tg);
read_contacts(opts,&tg);
INFO("Creating index...");
create_index(tgl, &tg, &opts);
LOG("Size of index: %lu\n", tgl.getSize());
//LOG("Depth: %u", tgl.get_log()->getDepth());
ofstream file;
LOG("Saving graph file in '%s'\n", opts.outfile);
file.open(opts.outfile, ios::binary);
tgl.save(file);
file.close();
return 0;
}
int main(int argc,char *argv[])
{
Centroid *SYS,*ENV;
Sprngmtx *Gamma;
char *sysfile,*envfile,*massfile,*ctfile,*spgfile;
double **GG;
double *CUT,**HS,**HE,**HX,**PH,*P;
double dd,x,y;
int **CT,**PIX,nss,nen,nn,ntp,nse,r1,c1,r2,c2,i,j,k;
int ptmd,rprm,pprm;
/* Formalities */
read_command_line(argc,argv,&pprm,&rprm,&ptmd,&MSCL);
/* Read coordinate and mass data */
sysfile=get_param(argv[pprm],"syscoords");
envfile=get_param(argv[pprm],"envcoords");
massfile=get_param(argv[pprm],"massfile");
SYS=read_centroids1(sysfile,massfile,&nss);
ENV=read_centroids1(envfile,massfile,&nen);
nn=nss+nen;
fprintf(stderr,"System read from %s: %d centroids\n",sysfile,nss);
fprintf(stderr,"Environment read from %s: %d centroids\n",envfile,nen);
fprintf(stderr,"Masses read from %s\n",massfile);
CT=imatrix(1,nn,1,nn);
/* Find extent of membrane */
membounds(ENV,nen,&MHI,&MLO);
/* Print masses, if called for */
if(ptmd==2){
for(i=1;i<=nss;i++)
for(j=-2;j<=0;j++){
k=3*i+j;
printf("%8d%8d% 25.15e\n",k,k,SYS[i].mass);
}
for(i=1;i<=nen;i++)
for(j=-2;j<=0;j++){
k=3*nss+3*i+j;
printf("%8d%8d% 25.15e\n",k,k,ENV[i].mass);
}
return 0;
}
/* ---------------- Assign contacts... ----------------- */
/* From a contact file... */
if((ctfile=get_param(argv[pprm],"contactfile"))!=NULL){
read_contacts(ctfile,CT,nn);
fprintf(stderr,"Contacts read from %s\n",ctfile);
}
/* ...or from a cutoff file... */
else if((ctfile=get_param(argv[pprm],"cutfile"))!=NULL){
fprintf(stderr,"Cutoff values read from %s\n",ctfile);
CUT=read_cutfile2(ctfile,SYS,ENV,nss,nen);
radius_contact_sysenv(CT,SYS,ENV,nss,nen,CUT);
}
/* ...or from default values */
else{
CUT=dvector(1,nn);
for(i=1;i<=nn;i++) CUT[i]=DEFCUT;
fprintf(stderr,"All cutoff values set to %.3f\n",DEFCUT);
radius_contact_sysenv(CT,SYS,ENV,nss,nen,CUT);
}
fprintf(stderr,"%d clusters\n",num_clusters(CT,nn));
if(ptmd==1){
fprintf(stderr,"Printing contacts\n");
for(i=1;i<=nn;i++)
for(j=i+1;j<=nn;j++)
if(CT[i][j]!=0)
printf("%d\t%d\n",i,j);
return 0;
}
/* ------- Construct the matrix of force constants -------*/
GG=dmatrix(1,nn,1,nn);
/* Read force constants from file... */
if((spgfile=get_param(argv[pprm],"springfile"))!=NULL){
fprintf(stderr,"Reading spring constants from %s\n",spgfile);
Gamma=read_springfile_sysenv(spgfile,SYS,ENV,nss,nen,&ntp);
spring_constants_sysenv(SYS,ENV,GG,CT,Gamma,nss,nen,ntp);
}
/* ...or else assign the default value to all springs */
else
for(i=1;i<=nn;i++)
for(j=i;j<=nn;j++)
if(CT[i][j]!=0)
GG[i][j]=GG[j][i]=DEFGAM;
/* Construct the mass-weighted Hessian from
coordinates, masses, and potential matrix */
fprintf(stderr,"Calculating Hessian...\n");
HS=dmatrix(1,3*nss,1,3*nss);
HE=dmatrix(1,3*nen,1,3*nen);
HX=dmatrix(1,3*nss,1,3*nen);
mwhess_sysenv(HS,HE,HX,SYS,ENV,GG,nss,nen);
/* PRINT THE ENVIRONMENT-ENVIRONMENT SUB-HESSIAN IN SPARSE FORMAT */
if(ptmd==0 && rprm==-1){
fprintf(stderr,"\nPrinting env-env sub-hessian...\n\n");
for(i=1;i<=3*nen;i++)
for(j=i;j<=3*nen;j++)
if(fabs(HE[i][j])>1.0e-10)
printf("%8d%8d% 25.15e\n",i,j,HE[i][j]);
return 0;
}
/* PRINT THE FULL HESSIAN IN SPARSE FORMAT */
if(ptmd==3){
for(i=1;i<=3*nss;i++){
for(j=i;j<=3*nss;j++)
if(fabs(HS[i][j])>1.0e-10)
printf("%8d%8d% 20.10e\n",i,j,HS[i][j]);
for(j=1;j<=3*nen;j++)
if(fabs(HX[i][j])>1.0e-10)
printf("%8d%8d% 20.10e\n",i,j+3*nss,HX[i][j]);
}
for(i=1;i<=3*nen;i++)
for(j=i;j<=3*nen;j++)
if(fabs(HE[i][j])>1.0e-10)
printf("%8d%8d% 20.10e\n",i+3*nss,j+3*nss,HE[i][j]);
return 0;
}
/* READ INVERSE OF ENVIRONMENTAL HESSIAN, OR INVERT HE */
free_imatrix(CT,1,nn,1,nn);
free_dmatrix(GG,1,nn,1,nn);
if(rprm!=-1){
fprintf(stderr,"Reading matrix from %s...\n",argv[rprm]);
read_sparsemtx(argv[rprm],HE,3*nen,3*nen);
}
else{
fprintf(stderr,"\nWell...How did I get here?\n\n");
exit(1);}
/* ---------------- CALCULATE AND PRINT THE PSEUDOHESSIAN ---------------- */
/* COUNT THE NUMBER OF NON-ZERO TERMS IN THE PROJECTION MATRIX */
nse=0;
for(i=1;i<=3*nss;i++)
for(j=1;j<=3*nen;j++)
if(fabs(HX[i][j])>1.0e-9) nse++;
fprintf(stderr,"%d non-zero projection elements\n",nse);
P=dvector(1,nse);
PIX=imatrix(1,nse,1,2);
k=1;
for(i=1;i<=3*nss;i++)
for(j=1;j<=3*nen;j++)
if(fabs(HX[i][j])>1.0e-9){
PIX[k][1]=i;
PIX[k][2]=j;
P[k]=HX[i][j];
k++;
}
free_dmatrix(HX,1,3*nss,1,3*nen);
PH=dmatrix(1,3*nss,1,3*nss);
for(i=1;i<=3*nss;i++)
for(j=i;j<=3*nss;j++)
PH[i][j]=PH[j][i]=0.0;
for(i=1;i<=nse;i++){
r1=PIX[i][1];
c1=PIX[i][2];
x=P[i];
for(j=i;j<=nse;j++){
r2=PIX[j][1];
c2=PIX[j][2];
y=HE[c1][c2]*P[j]*x;
PH[r1][r2]+=y;
if(r1==r2 && c1!=c2)
PH[r1][r2]+=y;
}
}
for(i=1;i<=3*nss;i++)
for(j=i;j<=3*nss;j++){
dd=HS[i][j]-PH[i][j];
if(fabs(dd)>1.0e-10)
printf("%8d%8d% 25.15e\n",i,j,dd);
}
return 0;
}
void ay_edit_local_accounts(void)
{
char *text[] = { _("C"),
_("Screen Name"),
_("Password"),
_("Service")
};
GtkWidget *box;
GtkWidget *window_box;
GtkWidget *hbox;
GtkWidget *button_box;
GtkWidget *label;
guint label_key;
GtkWidget *toolbar;
GtkToolItem *toolitem;
GtkToolItem *tool_sep;
GtkWidget *separator;
LList *list;
LList *l;
GtkAccelGroup *accel_group;
GtkCellRenderer *renderer;
GtkTreeViewColumn *column;
GtkTreeSelection *selection;
if (is_open)
return;
is_open = 1;
accel_group = gtk_accel_group_new();
account_window = gtk_window_new(GTK_WINDOW_TOPLEVEL);
gtk_window_set_position(GTK_WINDOW(account_window), GTK_WIN_POS_MOUSE);
gtk_widget_realize(account_window);
account_list_store = gtk_list_store_new(COL_COUNT,
G_TYPE_BOOLEAN, G_TYPE_STRING, G_TYPE_STRING, G_TYPE_STRING);
account_list =
gtk_tree_view_new_with_model(GTK_TREE_MODEL
(account_list_store));
renderer = gtk_cell_renderer_toggle_new();
column = gtk_tree_view_column_new_with_attributes(text[CONNECT],
renderer, "active", CONNECT, NULL);
gtk_tree_view_append_column(GTK_TREE_VIEW(account_list), column);
renderer = gtk_cell_renderer_text_new();
column = gtk_tree_view_column_new_with_attributes(text[USER_NAME],
renderer, "text", USER_NAME, NULL);
gtk_tree_view_column_set_sizing(column, GTK_TREE_VIEW_COLUMN_AUTOSIZE);
gtk_tree_view_append_column(GTK_TREE_VIEW(account_list), column);
renderer = gtk_cell_renderer_text_new();
column = gtk_tree_view_column_new_with_attributes(text[SERVICE_TYPE],
renderer, "text", SERVICE_TYPE, NULL);
gtk_tree_view_append_column(GTK_TREE_VIEW(account_list), column);
selection = gtk_tree_view_get_selection(GTK_TREE_VIEW(account_list));
gtk_tree_selection_set_mode(selection, GTK_SELECTION_MULTIPLE);
gtk_container_set_border_width(GTK_CONTAINER(account_window), 5);
g_signal_connect(selection, "changed",
G_CALLBACK(selection_made_callback), NULL);
box = gtk_vbox_new(FALSE, 0);
window_box = gtk_vbox_new(FALSE, 5);
hbox = gtk_hbox_new(FALSE, 5);
gtk_container_set_border_width(GTK_CONTAINER(hbox), 5);
/*Screen Name Section */
label = gtk_label_new_with_mnemonic(_("Screen _Name:"));
label_key = gtk_label_get_mnemonic_keyval(GTK_LABEL(label));
gtk_misc_set_alignment(GTK_MISC(label), 0, 0.5);
gtk_box_pack_start(GTK_BOX(box), label, TRUE, TRUE, 5);
gtk_widget_show(label);
username = gtk_entry_new();
gtk_box_pack_start(GTK_BOX(box), username, FALSE, FALSE, 2);
gtk_widget_show(username);
gtk_widget_add_accelerator(username, "grab_focus", accel_group,
label_key, GDK_MOD1_MASK, (GtkAccelFlags) 0);
/*Password Section */
label = gtk_label_new_with_mnemonic(_("_Password:"******"grab_focus", accel_group,
label_key, GDK_MOD1_MASK, (GtkAccelFlags) 0);
/*Service Type Section */
label = gtk_label_new_with_mnemonic(_("Service _Type:"));
label_key = gtk_label_get_mnemonic_keyval(GTK_LABEL(label));
gtk_misc_set_alignment(GTK_MISC(label), 0, 0.5);
gtk_box_pack_start(GTK_BOX(box), label, TRUE, TRUE, 5);
gtk_widget_show(label);
service_type = gtk_combo_box_new_text();
list = get_service_list();
for (l = list; l; l = l_list_next(l)) {
char *label = l->data;
gtk_combo_box_append_text(GTK_COMBO_BOX(service_type), label);
}
l_list_free(list);
gtk_widget_show(service_type);
gtk_box_pack_start(GTK_BOX(box), service_type, FALSE, FALSE, 2);
gtk_widget_add_accelerator(service_type, "grab_focus", accel_group,
label_key, GDK_MOD1_MASK, (GtkAccelFlags) 0);
/*Connect at startup Section */
connect_at_startup =
gtk_check_button_new_with_mnemonic(_("_Connect at startup"));
label_key =
gtk_label_get_mnemonic_keyval(GTK_LABEL(GTK_BIN
(connect_at_startup)->child));
gtk_widget_show(connect_at_startup);
gtk_widget_add_accelerator(connect_at_startup, "clicked", accel_group,
label_key, GDK_MOD1_MASK, (GtkAccelFlags) 0);
gtk_box_pack_start(GTK_BOX(box), connect_at_startup, FALSE, FALSE, 5);
gtk_box_pack_start(GTK_BOX(hbox), box, FALSE, FALSE, 2);
gtk_widget_show(box);
box = gtk_vbox_new(FALSE, 0);
read_contacts();
gtk_box_pack_start(GTK_BOX(box), account_list, TRUE, TRUE, 0);
gtk_widget_show(account_list);
gtk_box_pack_start(GTK_BOX(hbox), box, TRUE, TRUE, 2);
gtk_widget_show(box);
gtk_box_pack_start(GTK_BOX(window_box), hbox, TRUE, TRUE, 0);
gtk_widget_show(hbox);
separator = gtk_hseparator_new();
gtk_box_pack_start(GTK_BOX(window_box), separator, TRUE, TRUE, 0);
gtk_widget_show(separator);
/*Initialize Toolbar */
toolbar = gtk_toolbar_new();
gtk_toolbar_set_style(GTK_TOOLBAR(toolbar), GTK_TOOLBAR_BOTH);
gtk_toolbar_set_show_arrow(GTK_TOOLBAR(toolbar), FALSE);
gtk_toolbar_set_orientation(GTK_TOOLBAR(toolbar),
GTK_ORIENTATION_HORIZONTAL);
gtk_container_set_border_width(GTK_CONTAINER(toolbar), 0);
/*Add Button */
#define TOOLBAR_APPEND(titem,stock,tip,callback,cb_data) { \
titem = gtk_tool_button_new_from_stock(stock); \
gtk_tool_item_set_tooltip_text(titem, tip); \
g_signal_connect(titem, "clicked", G_CALLBACK(callback), cb_data); \
gtk_widget_show(GTK_WIDGET(titem)); \
gtk_toolbar_insert(GTK_TOOLBAR(toolbar), titem, -1); \
}
/* line will tell whether to draw the separator line or not */
#define TOOLBAR_APPEND_SEPARATOR(line) { \
tool_sep = gtk_separator_tool_item_new(); \
gtk_separator_tool_item_set_draw(GTK_SEPARATOR_TOOL_ITEM(tool_sep), line); \
gtk_widget_show(GTK_WIDGET(tool_sep)); \
gtk_toolbar_insert(GTK_TOOLBAR(toolbar), tool_sep, -1); \
}
TOOLBAR_APPEND(toolitem, GTK_STOCK_HELP, _("Help"), help_callback,
NULL);
TOOLBAR_APPEND_SEPARATOR(TRUE);
TOOLBAR_APPEND(toolitem, GTK_STOCK_ADD, _("Add Account"), add_callback,
NULL);
TOOLBAR_APPEND_SEPARATOR(FALSE);
/*Delete Button */
TOOLBAR_APPEND(del_button, GTK_STOCK_DELETE, _("Delete Account"),
remove_callback, NULL);
gtk_widget_set_sensitive(GTK_WIDGET(del_button), FALSE);
TOOLBAR_APPEND_SEPARATOR(FALSE);
/* Modify Button */
TOOLBAR_APPEND(mod_button, GTK_STOCK_EDIT, _("Modify Account"),
modify_callback, NULL);
gtk_widget_set_sensitive(GTK_WIDGET(mod_button), FALSE);
TOOLBAR_APPEND_SEPARATOR(TRUE);
/*Okay Button */
TOOLBAR_APPEND(toolitem, GTK_STOCK_OK, _("Ok"), ok_callback, NULL);
TOOLBAR_APPEND_SEPARATOR(FALSE);
/*Cancel Button */
TOOLBAR_APPEND(toolitem, GTK_STOCK_CANCEL, _("Cancel"), cancel_callback,
NULL);
#undef TOOLBAR_APPEND_SEPARATOR
#undef TOOLBAR_APPEND
/*Buttons End */
button_box = gtk_hbox_new(FALSE, 0);
gtk_box_pack_end(GTK_BOX(button_box), toolbar, FALSE, FALSE, 0);
gtk_widget_show(toolbar);
gtk_box_pack_start(GTK_BOX(window_box), button_box, FALSE, FALSE, 0);
gtk_widget_show(button_box);
gtk_widget_show(window_box);
gtk_container_add(GTK_CONTAINER(account_window), window_box);
gtk_window_set_title(GTK_WINDOW(account_window),
_("Ayttm Account Editor"));
g_signal_connect(account_window, "destroy", G_CALLBACK(destroy), NULL);
gtk_window_add_accel_group(GTK_WINDOW(account_window), accel_group);
gtk_widget_show(account_window);
gtk_widget_grab_focus(username);
}
