Create abf::setup_output() for consistency

doc/cvscript-fix-modify.tex

@@ -326,11 +326,11 @@
 \begin{mdexampleinput}{}
 \texttt{\textbf{fix\_modify Colvars save <prefix>}}
 \\
-\-~~~~\texttt{Change the prefix of all output files and save them}
+\-~~~~\texttt{Save the current state to a restart file with the given prefix}
 \\
 \-~~~~\texttt{\textbf{Parameters}}
 \\
-\-~~~~\texttt{prefix : string - Output prefix with trailing ".colvars.state" gets removed)}
+\-~~~~\texttt{prefix : string - Output prefix (trailing ".colvars.state" gets removed)}
 \end{mdexampleinput}
 \begin{mdexampleinput}{}
 \texttt{\textbf{fix\_modify Colvars savetostring}}
@@ -342,6 +342,15 @@
 \-~~~~\texttt{state : string - The saved state}
 \end{mdexampleinput}
 \begin{mdexampleinput}{}
+\texttt{\textbf{fix\_modify Colvars outputprefix [prefix]}}
+\\
+\-~~~~\texttt{Get/set the prefix for all output files}
+\\
+\-~~~~\texttt{\textbf{Parameters}}
+\\
+\-~~~~\texttt{prefix : string - Output prefix (trailing ".colvars.state" gets removed) (optional)}
+\end{mdexampleinput}
+\begin{mdexampleinput}{}
 \texttt{\textbf{fix\_modify Colvars targettemperature [T]}}
 \\
 \-~~~~\texttt{Get/set target temperature, overriding internally what the MD engine reports}
@@ -718,6 +727,15 @@
 \-~~~~\texttt{state : string - The bias state}
 \end{mdexampleinput}
 \begin{mdexampleinput}{}
+\texttt{\textbf{fix\_modify Colvars bias name writeoutput <prefix>}}
+\\
+\-~~~~\texttt{Write output data into files with the given prefix}
+\\
+\-~~~~\texttt{\textbf{Parameters}}
+\\
+\-~~~~\texttt{prefix : string - Prefix for the output files of this bias}
+\end{mdexampleinput}
+\begin{mdexampleinput}{}
 \texttt{\textbf{fix\_modify Colvars bias name set <feature> <value>}}
 \\
 \-~~~~\texttt{Set the given feature of this bias to a new value}

doc/cvscript-tcl.tex

@@ -326,11 +326,11 @@
 \begin{mdexampleinput}{}
 \texttt{\textbf{cv save <prefix>}}
 \\
-\-~~~~\texttt{Change the prefix of all output files and save them}
+\-~~~~\texttt{Save the current state to a restart file with the given prefix}
 \\
 \-~~~~\texttt{\textbf{Parameters}}
 \\
-\-~~~~\texttt{prefix : string - Output prefix with trailing ".colvars.state" gets removed)}
+\-~~~~\texttt{prefix : string - Output prefix (trailing ".colvars.state" gets removed)}
 \end{mdexampleinput}
 \begin{mdexampleinput}{}
 \texttt{\textbf{cv savetostring}}
@@ -342,6 +342,15 @@
 \-~~~~\texttt{state : string - The saved state}
 \end{mdexampleinput}
 \begin{mdexampleinput}{}
+\texttt{\textbf{cv outputprefix [prefix]}}
+\\
+\-~~~~\texttt{Get/set the prefix for all output files}
+\\
+\-~~~~\texttt{\textbf{Parameters}}
+\\
+\-~~~~\texttt{prefix : string - Output prefix (trailing ".colvars.state" gets removed) (optional)}
+\end{mdexampleinput}
+\begin{mdexampleinput}{}
 \texttt{\textbf{cv targettemperature [T]}}
 \\
 \-~~~~\texttt{Get/set target temperature, overriding internally what the MD engine reports}
@@ -718,6 +727,15 @@
 \-~~~~\texttt{state : string - The bias state}
 \end{mdexampleinput}
 \begin{mdexampleinput}{}
+\texttt{\textbf{cv bias name writeoutput <prefix>}}
+\\
+\-~~~~\texttt{Write output data into files with the given prefix}
+\\
+\-~~~~\texttt{\textbf{Parameters}}
+\\
+\-~~~~\texttt{prefix : string - Prefix for the output files of this bias}
+\end{mdexampleinput}
+\begin{mdexampleinput}{}
 \texttt{\textbf{cv bias name set <feature> <value>}}
 \\
 \-~~~~\texttt{Set the given feature of this bias to a new value}

namd/src/colvarproxy_namd.C

@@ -363,6 +363,9 @@ void colvarproxy_namd::calculate()
       b_simulation_continuing = true;
 
       // Update NAMD output and restart prefixes
+      // FIXME: this overrides any change done via cv scripting
+      // should the cv outputprefix be disabled in NAMD?
+      // Should we detect a manual setting?
       colvarproxy_io::set_output_prefix(std::string(simparams->outputFilename));
       colvarproxy_io::set_restart_output_prefix(std::string(simparams->restartFilename));
       colvarproxy_io::set_default_restart_frequency(simparams->restartFrequency);

src/colvarbias_abf.cpp

@@ -411,14 +411,6 @@ int colvarbias_abf::update()
   // *********************************
 
 
-  // update the output prefix; TODO: move later to setup_output() function
-  if (cvm::main()->num_biases_feature(colvardeps::f_cvb_calc_pmf) == 1) {
-    // This is the only bias computing PMFs
-    output_prefix = cvm::output_prefix();
-  } else {
-    output_prefix = cvm::output_prefix() + "." + this->name;
-  }
-
 
   // update UI estimator every step
   if (b_UI_estimator)
@@ -430,7 +422,6 @@ int colvarbias_abf::update()
       x[i] = colvars[i]->actual_value();
       y[i] = colvars[i]->value();
     }
-    eabf_UI.update_output_filename(output_prefix);
     eabf_UI.update(cvm::step_absolute(), x, y);
   }
 
@@ -720,6 +711,20 @@ size_t colvarbias_abf::replica_share_freq() const
   return shared_freq;
 }
 
+int colvarbias_abf::setup_output()
+{
+  // update the output prefix
+  if (cvm::main()->num_biases_feature(colvardeps::f_cvb_calc_pmf) == 1) {
+    // This is the only bias computing PMFs
+    output_prefix = cvm::output_prefix();
+  } else {
+    output_prefix = cvm::output_prefix() + "." + this->name;
+  }
+  if (b_UI_estimator)
+    eabf_UI.update_output_filename(output_prefix);
+
+  return COLVARS_OK;
+}
 
 template <class T> int colvarbias_abf::write_grid_to_file(T const *grid,
                                                           std::string const &filename,

src/colvarbias_abf.h

@@ -37,6 +37,7 @@ class colvarbias_abf : public colvarbias {
   ~colvarbias_abf() override;
   /// Per-timestep update of ABF bias
   int update() override;
+  int setup_output() override;
 
 private:
 

src/colvarproxy_io.h

@@ -165,6 +165,9 @@ class colvarproxy_io {
   /// Default prefix to be used for all output files (final configuration)
   std::string output_prefix_str;
 
+  /// The output prefix obtained from the backend was overridden manually via scripting
+  bool b_override_output_prefix = false;
+
   /// Prefix of the restart (checkpoint) file to be written next
   std::string restart_output_prefix_str;
 

src/colvarscript_commands.h

@@ -570,16 +570,12 @@ CVSCRIPT(cv_resetindexgroups,
          )
 
 CVSCRIPT(cv_save,
-         "Change the prefix of all output files and save them",
+         "Save the current state to a restart file with the given prefix",
          1, 1,
-         "prefix : string - Output prefix with trailing \".colvars.state\" gets removed)",
+         "prefix : string - Output prefix (trailing \".colvars.state\" gets removed)",
          std::string const prefix =
            cvm::state_file_prefix(script->obj_to_str(script->get_module_cmd_arg(0, objc, objv)));
-         int error_code = script->proxy()->set_output_prefix(prefix);
-         error_code |= script->module()->setup_output();
-         error_code |= script->module()->write_restart_file(prefix+
-                                                            ".colvars.state");
-         error_code |= script->module()->write_output_files();
+         int error_code = script->module()->write_restart_file(prefix + ".colvars.state");
          return error_code;
          )
 
@@ -591,6 +587,24 @@ CVSCRIPT(cv_savetostring,
          return script->module()->write_restart_string(script->modify_str_result());
          )
 
+CVSCRIPT(cv_outputprefix,
+         "Get/set the prefix for all output files",
+         0, 1,
+         "prefix : string - Output prefix (trailing \".colvars.state\" gets removed)",
+         char const *argstr =
+           script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
+         if (argstr) {
+           std::string const prefix = cvm::state_file_prefix(argstr);
+           cvm::log("Setting output prefix to " + prefix);
+           int error = cvm::proxy->set_output_prefix(prefix);
+           error |= script->module()->setup_output();
+           return error;
+         } else {
+           script->set_result_str(cvm::output_prefix());
+           return COLVARS_OK;
+         }
+         )
+
 CVSCRIPT(cv_targettemperature,
          "Get/set target temperature, overriding internally what the MD engine reports\n"
          "T : float - Current target temperature in K",

src/colvarscript_commands_bias.h

@@ -164,6 +164,21 @@ CVSCRIPT(bias_savetostring,
          return this_bias->write_state_string(script->modify_str_result());
          )
 
+CVSCRIPT(bias_writeoutput,
+         "Write output data into files with the given prefix",
+         1, 1,
+         "prefix : string - Prefix for the output files of this bias",
+         std::string const prefix =
+          cvm::state_file_prefix(script->obj_to_str(script->get_bias_cmd_arg(0, objc, objv)));
+         std::string prefix_bak = cvm::output_prefix();
+         cvm::proxy->set_output_prefix(prefix);
+         this_bias->setup_output();
+         int error_code = this_bias->write_output_files();
+         cvm::proxy->set_output_prefix(prefix_bak);
+         this_bias->setup_output();
+         return error_code;
+         )
+
 CVSCRIPT(bias_set,
          "Set the given feature of this bias to a new value",
          2, 2,

tests/unittests/embedded_tcl.cpp

@@ -19,6 +19,7 @@ extern "C" int main(int argc, char *argv[]) {
     return 1;
   }
 
+  proxy->tcl_run_script("puts \"(Tcl) This is Tcl version [info tclversion]\"");
   proxy->tcl_run_script("puts \"(Tcl) Currently defined variables:\n(Tcl) [info vars]\"");
   proxy->tcl_run_script("puts \"(Tcl) Currently defined procedures:\n(Tcl) [info procs]\"");