added easy restart feature.

.gitignore

@@ -58,4 +58,5 @@ src/gui/build-*
 src/gui/*.o
 src/gui/gui_mcmd.pro.user.*
 src/buildgui
-
+saved_data
+saved_data/*

src/classes.cpp

@@ -105,6 +105,7 @@ class Constants {
         double dist_within_radius; // the radius within which to search from origin
         int_fast8_t histogram_option = 1; // output histogram data which can be plotted in VMD
         int_fast8_t autocenter = 1; // center all atoms about origin automatically. can opt out of it.
+        int_fast8_t restart_mode = 0; // option to restart job automatically (by searching for restart.pdb)
         int_fast8_t no_zero_option = 0; // option to disallow zero sorbates in the simulation. default off.
         int_fast8_t simulated_annealing = 0; // sim. ann.
         double sa_target = 0.0; // target temperature for annealing.

src/io.cpp

@@ -858,6 +858,10 @@ void readInput(System &system, char* filename) {
 				system.constants.jobname = lc[1].c_str();
 				std::cout << "Got job name = " << lc[1].c_str(); printf("\n");
 
+            } else if (!strcasecmp(lc[0].c_str(),"restart")) {
+                system.constants.restart_mode = 1;
+                std::cout << "Got restart option = " << lc[1].c_str(); printf("\n");
+
 			} else if (!strcasecmp(lc[0].c_str(), "mode")) {
 				system.constants.mode = lc[1].c_str();
 				std::cout << "Got mode = " << lc[1].c_str(); printf("\n");
@@ -1580,6 +1584,10 @@ void inputValidation(System &system) {
         std::cout << "ERROR: You turned the crystal-builder on but did not specify a (correct) dimension to duplicate. e.g., `crystalbuild_y 2` is acceptable but `crystalbuild_y 0` is not. Leave the option off if you don't want to use it. (i.e. x y z are set to 1 by default).";
         exit(EXIT_FAILURE);
     }
+    if (e == ENSEMBLE_UVT && system.stats.count_movables <= 0 && system.constants.sorbate_name.size() ==0) {
+        std::cout << "ERROR: You specified uVT with a system containing no movable molecules and did not specify a desired sorbate. Try `sorbate_name h2_bssp`, for example.";
+        exit(EXIT_FAILURE);
+    }
 
 }
 // end input validation function

src/main.cpp

@@ -23,6 +23,7 @@
 #include <stdlib.h>
 #include <time.h>
 #include <chrono>
+#include <sys/stat.h>
 //#include <float.h>
 
 // Windows compilation (c11 instead of c++) doesn't auto-define pi.
@@ -126,7 +127,20 @@ int main(int argc, char **argv) {
     System system;
 	system.checkpoint("setting up system with main functions...");
     readInput(system, argv[1]); // executable takes the input file as only argument.
-	readInAtoms(system, system.constants.atom_file);
+	if (system.constants.restart_mode) {
+        // restarting an old job. Make a new saved_data folder e.g. "saved_data4" then overwrite the input file.
+        int save_folder_number=1;
+        struct stat sb;
+        string folder_name = "saved_data"+to_string(save_folder_number);
+        while (stat(folder_name.c_str(), &sb) == 0 && S_ISDIR(sb.st_mode)) {
+            save_folder_number++;
+            folder_name = "saved_data"+to_string(save_folder_number);
+        }
+        string command = "mkdir "+folder_name+"; cp * "+folder_name+"; cp restart.pdb "+system.constants.atom_file.c_str();
+        int whatever=std::system(command.c_str());
+        printf("RESTARTING previous job from input atoms contained in %s/restart.pdb\n",folder_name.c_str());
+    }
+    readInAtoms(system, system.constants.atom_file);
 	paramOverrideCheck(system);
 	if (system.constants.autocenter)
         centerCoordinates(system);