when reading binary init, only read u unless using the 'resume' command.

In particular, removed the 'init_flow' parameter

src/main.c

@@ -63,7 +63,6 @@ typedef struct nstrophy_parameters {
   FILE* drivingfile;
   double lyapunov_reset;
   unsigned int lyapunov_trigger;
-  bool init_flow_file;
   bool print_alpha;
 } nstrophy_parameters;
 
@@ -85,7 +84,7 @@ _Complex double* set_driving(nstrophy_parameters parameters);
 // set initial condition
 _Complex double* set_init(nstrophy_parameters* parameters);
 // set initial tangent flow for lyapunov exponents
-int set_lyapunov_flow_init( double** lyapunov_flow0, double** lyapunov_avg0, double* lyapunov_prevtime, double* lyapunov_startingtime, nstrophy_parameters parameters);
+int set_lyapunov_flow_init( double** lyapunov_flow0, double** lyapunov_avg0, double* lyapunov_prevtime, double* lyapunov_startingtime, bool fromfile, nstrophy_parameters parameters);
 
 // signal handler
 void sig_handler (int signo);
@@ -130,6 +129,7 @@ int main (
   dstring resumefile_str;
   FILE* savefile=NULL;
   FILE* utfile=NULL;
+  bool resume=false;
 
   command=0;
 
@@ -169,6 +169,8 @@ int main (
 
   // if command is 'resume', then read args from file
   if(command==COMMAND_RESUME){
+    // remember that the original command was resume (to set values from init file)
+    resume=true;
     ret=args_from_file(&param_str, &command, &nthreads, &savefile_str, &utfile_str, dstring_to_str_noinit(&resumefile_str));
     if(ret<0){
       dstring_free(param_str);
@@ -232,9 +234,19 @@ int main (
   g=set_driving(parameters);
   // set initial condition
   u0=set_init(&parameters);
+  // read extra values from init file when resuming a computation
+  if(resume){
+    // read start time
+    fread(&(parameters.starting_time), sizeof(double), 1, parameters.initfile);
+    // if adaptive step algorithm
+    if(parameters.algorithm>ALGORITHM_ADAPTIVE_THRESHOLD){
+      // read delta
+      fread(&(parameters.delta), sizeof(double), 1, parameters.initfile);
+    }
+  }
   // set initial condition for the lyapunov flow
   if (command==COMMAND_LYAPUNOV){
-    set_lyapunov_flow_init(&lyapunov_flow0, &lyapunov_avg0, &lyapunov_prevtime, &lyapunov_startingtime, parameters);
+    set_lyapunov_flow_init(&lyapunov_flow0, &lyapunov_avg0, &lyapunov_prevtime, &lyapunov_startingtime, resume, parameters);
   }
 
   // if init_enstrophy is not set in the parameters, then compute it from the initial condition
@@ -607,7 +619,6 @@ int set_default_params(
   parameters->algorithm_lyapunov=ALGORITHM_RK4;
   // default lyapunov_reset will be print_time (set later) for now set target to 0 to indicate it hasn't been set explicitly
   parameters->lyapunov_trigger=0;
-  parameters->init_flow_file=false;
 
   parameters->print_alpha=false;
   
@@ -686,12 +697,6 @@ int read_params(
     parameters->lyapunov_reset=parameters->print_freq;
   }
 
-  // check that if flow_init is used, then so is init
-  if(parameters->init_flow_file && parameters->init!=INIT_FILE){
-    fprintf(stderr, "error: cannot use 'init_flow:file' if 'init' is not a binary file\n");
-    return(-1);
-  }
-
   return(0);
 }
 
@@ -1011,16 +1016,6 @@ int set_parameter(
       return(-1);
     }
   }
-  else if (strcmp(lhs,"init_flow")==0){
-    if(strcmp(rhs,"file")==0){
-      parameters->init_flow_file=true;
-    } else if (strcmp(rhs,"identity")==0){
-      parameters->init_flow_file=false;
-    } else {
-      fprintf(stderr, "error: parameter 'init_flow' should be 'file' or 'identity'\n       got '%s'\n",rhs);
-      return(-1);
-    }
-  }
   else{
     fprintf(stderr, "error: unrecognized parameter '%s'\n",lhs);
     return(-1);
@@ -1136,12 +1131,6 @@ _Complex double* set_init(
 
   case INIT_FILE:
     init_file_bin(u0, parameters->K1, parameters->K2, parameters->initfile);
-    // read start time
-    fread(&(parameters->starting_time), sizeof(double), 1, parameters->initfile);
-    if(parameters->algorithm>ALGORITHM_ADAPTIVE_THRESHOLD){
-      // read delta
-      fread(&(parameters->delta), sizeof(double), 1, parameters->initfile);
-    }
     break;
 
   case INIT_FILE_TXT:
@@ -1183,12 +1172,14 @@ int set_lyapunov_flow_init(
   double** lyapunov_avg0,
   double* lyapunov_prevtime,
   double* lyapunov_startingtime,
+  bool fromfile, // whether to initialize from file
   nstrophy_parameters parameters
 ){
   *lyapunov_flow0=calloc(4*(parameters.K1*(2*parameters.K2+1)+parameters.K2)*(parameters.K1*(2*parameters.K2+1)+parameters.K2),sizeof(double));
   *lyapunov_avg0=calloc(2*(parameters.K1*(2*parameters.K2+1)+parameters.K2),sizeof(double));
 
-  if(parameters.init_flow_file){
+  // read from file or init from identity matrix
+  if(fromfile){
     // read flow
     read_mat2_bin(*lyapunov_flow0, parameters.K1, parameters.K2, parameters.initfile);
     // read time of last QR decomposition