Combine NPMC, GMC, LGMC

GMC/reaction_network.h

@@ -19,8 +19,6 @@ struct Reaction {
     double rate;
 };
 
-
-
 // parameters passed to the ReactionNetwork constructor
 // by the dispatcher which are model specific
 struct ReactionNetworkParameters {
@@ -38,6 +36,8 @@ struct ReactionNetwork {
     // maps species to the reactions which involve that species
     std::vector<std::vector<int>> dependents;
 
+    ReactionNetwork();
+
     ReactionNetwork(
         SqlConnection &reaction_network_database,
         SqlConnection &initial_state_database,

GMC/sql_types.h

@@ -46,51 +46,6 @@ void ReactionSql::action(ReactionSql &r, sqlite3_stmt *stmt) {
         r.rate = sqlite3_column_double(stmt, 7);
 };
 
-struct LatticeReactionSql {
-    unsigned long int reaction_id;
-    int number_of_reactants;
-    int number_of_products;
-    int reactant_1;
-    int reactant_2;
-    int product_1;
-    int product_2;
-    double rate;
-    double dG;
-    double reorganization;
-    char phase_reactant_1;
-    char phase_reactant_2;
-    char phase_product_1;
-    char phase_product_2;
-    char type;
-    static std::string sql_statement;
-    static void action(LatticeReactionSql &r, sqlite3_stmt *stmt);
-};
-
-std::string LatticeReactionSql::sql_statement =
-    "SELECT reaction_id, number_of_reactants, number_of_products, "
-    "reactant_1, reactant_2, product_1, product_2, rate, dG, "
-    "reorganization, phase_reactant_1, phase_reactant_2, "
-    "phase_product_1, phase_product_2, type FROM reactions;";
-
-
-void LatticeReactionSql::action(LatticeReactionSql &r, sqlite3_stmt *stmt) {
-        r.reaction_id = sqlite3_column_int(stmt, 0);
-        r.number_of_reactants = sqlite3_column_int(stmt, 1);
-        r.number_of_products = sqlite3_column_int(stmt, 2);
-        r.reactant_1 = sqlite3_column_int(stmt, 3);
-        r.reactant_2 = sqlite3_column_int(stmt, 4);
-        r.product_1 = sqlite3_column_int(stmt, 5);
-        r.product_2 = sqlite3_column_int(stmt, 6);
-        r.rate = sqlite3_column_double(stmt, 7);
-        r.dG = sqlite3_column_double(stmt, 8);
-        r.reorganization = sqlite3_column_double(stmt, 9);
-        r.phase_reactant_1 = sqlite3_column_double(stmt, 10);
-        r.phase_reactant_2 = sqlite3_column_double(stmt, 11);
-        r.phase_product_1 = sqlite3_column_double(stmt, 12);
-        r.phase_product_2 = sqlite3_column_double(stmt, 13);
-        r.type = sqlite3_column_double(stmt, 14);
-};
-
 
 struct InitialStateSql {
     int species_id;

LGMC/LGMC.cpp

@@ -15,7 +15,7 @@ void print_usage() {
               << "number_of_simulations\n"
               << "base_seed\n"
               << "step_cutoff\n"
-              << "lattice_parameters\n";
+              << "parameters\n";
 
 } // print_usage()
 
@@ -34,6 +34,7 @@ void print_usage_LGMC_parameters() {
               << "Periodicity in z dimension (T/F)\n"
               << "Temperature\n"
               << "Electron free energy\n"
+              << "Charge transfer style (M/B)\n"
               << "Is Add Site (T/F)\n";
 }
 
@@ -54,7 +55,7 @@ int main(int argc, char **argv) {
         //{"thread_count", required_argument, NULL, 5},
         {"step_cutoff", optional_argument, NULL, 6},
         {"time_cutoff", optional_argument, NULL, 7},
-        {"lattice_parameters", required_argument, NULL, 8},
+        {"parameters", required_argument, NULL, 8},
         {NULL, 0, NULL, 0}
         // last element of options array needs to be filled with zeros
     };
@@ -145,13 +146,15 @@ int main(int argc, char **argv) {
     float g_e;
     bool is_add_site;
     char add_site;
+    ChargeTransferStyle charge_transfer_style;
+    char ct_style;
 
 
     std::cin >> latconst >> boxxlo >> boxxhi >> boxylo >> boxyhi >> boxzlo >> boxzhi
-    >> xperiod >> yperiod >> zperiod >> temperature >> g_e >> add_site;
+    >> xperiod >> yperiod >> zperiod >> temperature >> g_e >> add_site >> ct_style;
 
     if(std::cin.fail()) {
-        std::cout << "Incorrect lattice file arguments.\n";
+        std::cout << "Incorrect parameter file arguments.\n";
         exit(EXIT_FAILURE);
     }
 
@@ -161,7 +164,7 @@ int main(int argc, char **argv) {
     else if (xperiod == 'F') {
         is_add_site = false;
     }else {
-        std::cout << "Incorrect lattice file argument for add site.\n";
+        std::cout << "Incorrect parameter file argument for add site.\n";
         exit(EXIT_FAILURE);
     }
 
@@ -171,7 +174,7 @@ int main(int argc, char **argv) {
     else if (xperiod == 'F') {
         xperiodic = false;
     }else {
-        std::cout << "Incorrect lattice file argument for x periodicity.\n";
+        std::cout << "Incorrect parameter file argument for x periodicity.\n";
         exit(EXIT_FAILURE);
     }
 
@@ -181,7 +184,7 @@ int main(int argc, char **argv) {
     else if (yperiod == 'F') {
         yperiodic = false;
     }else {
-        std::cout << "Incorrect lattice file argument for y periodicity.\n";
+        std::cout << "Incorrect parameter file argument for y periodicity.\n";
         exit(EXIT_FAILURE);
     }
 
@@ -191,19 +194,30 @@ int main(int argc, char **argv) {
     else if (zperiod == 'F') {
         zperiodic = false;
     }else {
-        std::cout << "Incorrect lattice file argument for z periodicity.\n";
+        std::cout << "Incorrect parameter file argument for z periodicity.\n";
+        exit(EXIT_FAILURE);
+    }
+
+    if(ct_style == 'M') {
+        charge_transfer_style = ChargeTransferStyle::MARCUS;
+    }
+    else if (ct_style == 'B') {
+        charge_transfer_style = ChargeTransferStyle::BUTLER_VOLMER;
+    }else {
+        std::cout << "Incorrect parameter file argument for charge transfer style.\n";
         exit(EXIT_FAILURE);
     }
 
 
     LGMCParameters parameters{.latconst = latconst, .boxxlo = boxxlo, .boxxhi = boxxhi, 
                               .boxylo = boxyhi, .boxzlo = boxzlo, .boxzhi = boxzhi, 
                               .xperiodic = xperiodic, .yperiodic = yperiodic, .zperiodic = zperiodic, 
-                              .temperature = temperature, .g_e = g_e, .is_add_sites = is_add_site};                               
+                              .temperature = temperature, .g_e = g_e, .is_add_sites = is_add_site,
+                              .charge_transfer_style = charge_transfer_style};                               
 
     Dispatcher<
         LatSolver,
-        LGMC_NS::LatticeReactionNetwork,
+        LatticeReactionNetwork,
         LGMCParameters,
         TrajectoriesSql
         >