BhallaLab · dilawar · May 31, 2019 · May 30, 2019 · May 30, 2019 · May 30, 2019
diff --git a/biophysics/Neuron.cpp b/biophysics/Neuron.cpp
diff --git a/builtins/CMakeLists.txt b/builtins/CMakeLists.txt
@@ -51,7 +51,8 @@ set(SRCS
     Arith.cpp
     Group.cpp
     Mstring.cpp
-    Func.cpp
+    # Func.cpp
+    MooseParser.cpp
     Function.cpp
     Variable.cpp
     InputVariable.cpp

diff --git a/builtins/Function.cpp b/builtins/Function.cpp
@@ -59,29 +59,29 @@ static const double TriggerThreshold = 0.0;
 static SrcFinfo1<double> *valueOut()
 {
     static SrcFinfo1<double> valueOut("valueOut",
-                                      "Evaluated value of the function for the current variable values.");
+            "Evaluated value of the function for the current variable values.");
     return &valueOut;
 }
 
 static SrcFinfo1< double > *derivativeOut()
 {
     static SrcFinfo1< double > derivativeOut("derivativeOut",
-                                             "Value of derivative of the function for the current variable values");
+            "Value of derivative of the function for the current variable values");
     return &derivativeOut;
 }
 
 static SrcFinfo1< double > *rateOut()
 {
     static SrcFinfo1< double > rateOut("rateOut",
-                                             "Value of time-derivative of the function for the current variable values");
+            "Value of time-derivative of the function for the current variable values");
     return &rateOut;
 }
 
 static SrcFinfo1< vector < double > *> *requestOut()
 {
     static SrcFinfo1< vector < double > * > requestOut(
-        "requestOut",
-        "Sends request for input variable from a field on target object");
+            "requestOut",
+            "Sends request for input variable from a field on target object");
     return &requestOut;
 
 }
@@ -168,8 +168,9 @@ const Cinfo * Function::initCinfo()
         "max         var.    max of all arguments\n"
         "sum         var.    sum of all arguments\n"
         "avg         var.    mean value of all arguments\n"
+        "rnd         0       rand(), random float between 0 and 1, honors global moose.seed.\n"
         "rand        1       rand(seed), random float between 0 and 1, \n"
-        "                    if seed = -1, then a 'random' seed is created.\n"
+        "                    if seed = -1, then a 'random' seed is used.\n"
         "rand2       3       rand(a, b, seed), random float between a and b, \n"
         "                    if seed = -1, a 'random' seed is created using either\n"
         "                    by random_device or by reading system clock\n"
@@ -235,89 +236,89 @@ const Cinfo * Function::initCinfo()
     // Shared messages
     ///////////////////////////////////////////////////////////////////
     static DestFinfo process( "process",
-                              "Handles process call, updates internal time stamp.",
-                              new ProcOpFunc< Function >( &Function::process ) );
+            "Handles process call, updates internal time stamp.",
+            new ProcOpFunc< Function >( &Function::process ) );
     static DestFinfo reinit( "reinit",
-                             "Handles reinit call.",
-                             new ProcOpFunc< Function >( &Function::reinit ) );
+            "Handles reinit call.",
+            new ProcOpFunc< Function >( &Function::reinit ) );
     static Finfo* processShared[] = { &process, &reinit };
 
     static SharedFinfo proc( "proc",
-                             "This is a shared message to receive Process messages "
-                             "from the scheduler objects."
-                             "The first entry in the shared msg is a MsgDest "
-                             "for the Process operation. It has a single argument, "
-                             "ProcInfo, which holds lots of information about current "
-                             "time, thread, dt and so on. The second entry is a MsgDest "
-                             "for the Reinit operation. It also uses ProcInfo. ",
-                             processShared, sizeof( processShared ) / sizeof( Finfo* )
-                             );
-	/*
-    static DestFinfo trigger( "trigger",
-		"Handles trigger input. Argument is timestamp of event. This is "
-		"compatible with spike events as well as chemical ones. ",
-        new OpFunc1< Function, double >( &Function::trigger ) );
-		*/
+            "This is a shared message to receive Process messages "
+            "from the scheduler objects."
+            "The first entry in the shared msg is a MsgDest "
+            "for the Process operation. It has a single argument, "
+            "ProcInfo, which holds lots of information about current "
+            "time, thread, dt and so on. The second entry is a MsgDest "
+            "for the Reinit operation. It also uses ProcInfo. ",
+            processShared, sizeof( processShared ) / sizeof( Finfo* )
+            );
+    /*
+       static DestFinfo trigger( "trigger",
+       "Handles trigger input. Argument is timestamp of event. This is "
+       "compatible with spike events as well as chemical ones. ",
+       new OpFunc1< Function, double >( &Function::trigger ) );
+       */
 
     static Finfo *functionFinfos[] =
-            {
-                &value,
-                &rate,
-                &derivative,
-                &mode,
-				&useTrigger,
-				&doEvalAtReinit,
-                &expr,
-                &numVars,
-                &inputs,
-                &constants,
-                &independent,
-                &proc,
-                requestOut(),
-                valueOut(),
-                rateOut(),
-                derivativeOut(),
-            };
+    {
+        &value,
+        &rate,
+        &derivative,
+        &mode,
+        &useTrigger,
+        &doEvalAtReinit,
+        &expr,
+        &numVars,
+        &inputs,
+        &constants,
+        &independent,
+        &proc,
+        requestOut(),
+        valueOut(),
+        rateOut(),
+        derivativeOut(),
+    };
 
     static string doc[] =
-            {
-                "Name", "Function",
-                "Author", "Subhasis Ray",
-                "Description",
-                "General purpose function calculator using real numbers.\n"
-                "It can parse mathematical expression defining a function and evaluate"
-                " it and/or its derivative for specified variable values."
-                "You can assign expressions of the form::\n"
-                "\n"
-                "f(c0, c1, ..., cM, x0, x1, ..., xN, y0,..., yP ) \n"
-                "\n"
-                " where `ci`'s are constants and `xi`'s and `yi`'s are variables."
-
-                "The constants must be defined before setting the expression and"
-                " variables are connected via messages. The constants can have any"
-                " name, but the variable names must be of the form x{i} or y{i}"
-                "  where i is increasing integer starting from 0.\n"
-                " The variables can be input from other moose objects."
-                " Such variables must be named `x{i}` in the expression and the source"
-                " field is connected to Function.x[i]'s `input` destination field.\n"
-                " In case the input variable is not available as a source field, but is"
-                " a value field, then the value can be requested by connecting the"
-                " `requestOut` message to the `get{Field}` destination on the target"
-                " object. Such variables must be specified in the expression as y{i}"
-                " and connecting the messages should happen in the same order as the"
-                " y indices.\n"
-                " This class handles only real numbers (C-double). Predefined constants"
-                " are: pi=3.141592..., e=2.718281..."
-            };
+    {
+        "Name", "Function",
+        "Author", "Subhasis Ray",
+        "Description",
+        "General purpose function calculator using real numbers.\n"
+            "It can parse mathematical expression defining a function and evaluate"
+            " it and/or its derivative for specified variable values."
+            "You can assign expressions of the form::\n"
+            "\n"
+            "f(c0, c1, ..., cM, x0, x1, ..., xN, y0,..., yP ) \n"
+            "\n"
+            " where `ci`'s are constants and `xi`'s and `yi`'s are variables."
+
+            "The constants must be defined before setting the expression and"
+            " variables are connected via messages. The constants can have any"
+            " name, but the variable names must be of the form x{i} or y{i}"
+            "  where i is increasing integer starting from 0.\n"
+            " The variables can be input from other moose objects."
+            " Such variables must be named `x{i}` in the expression and the source"
+            " field is connected to Function.x[i]'s `input` destination field.\n"
+            " In case the input variable is not available as a source field, but is"
+            " a value field, then the value can be requested by connecting the"
+            " `requestOut` message to the `get{Field}` destination on the target"
+            " object. Such variables must be specified in the expression as y{i}"
+            " and connecting the messages should happen in the same order as the"
+            " y indices.\n"
+            " This class handles only real numbers (C-double). Predefined constants"
+            " are: pi=3.141592..., e=2.718281..."
+    };
 
     static Dinfo< Function > dinfo;
     static Cinfo functionCinfo("Function",
-                               Neutral::initCinfo(),
-                               functionFinfos,
-                               sizeof(functionFinfos) / sizeof(Finfo*),
-                               &dinfo,
-                               doc,
-                               sizeof(doc)/sizeof(string));
+            Neutral::initCinfo(),
+            functionFinfos,
+            sizeof(functionFinfos) / sizeof(Finfo*),
+            &dinfo,
+            doc,
+            sizeof(doc)/sizeof(string));
     return &functionCinfo;
 
 }

diff --git a/builtins/Function.h b/builtins/Function.h
@@ -12,43 +12,12 @@
 // URL:
 // Keywords:
 // Compatibility:
-//
-//
-
-// Commentary:
-//
-// A new version of Func with FieldElements to collect data.
-//
-//
-
-// Change log:
-//
-//
-//
-//
-// This program is free software; you can redistribute it and/or
-// modify it under the terms of the GNU General Public License as
-// published by the Free Software Foundation; either version 3, or
-// (at your option) any later version.
-//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-// General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with this program; see the file COPYING.  If not, write to
-// the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-// Floor, Boston, MA 02110-1301, USA.
-//
-//
 
-// Code:
 
 #ifndef _MOOSE_FUNCTION_H_
 #define _MOOSE_FUNCTION_H_
 
-#include "../external/muparser/include/muParser.h"
+#include "MooseParser.h"
 
 /**
    Simple function parser and evaluator for MOOSE. This can take a mathematical
@@ -158,7 +127,7 @@ class Function
     map< string, double *> _constbuf;  // for constants
     string _independent; // index of independent variable
 
-    mu::Parser _parser;
+    MooseParser _parser;
 
     void _clearBuffer();
     void _showError(mu::Parser::exception_type &e) const;

diff --git a/builtins/MooseParser.cpp b/builtins/MooseParser.cpp
@@ -0,0 +1,18 @@
+/***
+ *    Description:  Class MooseParser.  
+ *
+ *        Created:  2019-05-30
+
+ *         Author:  Dilawar Singh <[email protected]>
+ *   Organization:  NCBS Bangalore
+ *        License:  MIT License
+ */
+
+#include "MooseParser.h"
+
+MooseParser::MooseParser()
+{}
+
+MooseParser::~MooseParser()
+{}
+
diff --git a/builtins/MooseParser.h b/builtins/MooseParser.h
@@ -0,0 +1,26 @@
+/***
+ *    Description:  MooseParser class. 
+ *
+ *        Created:  2019-05-30
+
+ *         Author:  Dilawar Singh <[email protected]>
+ *   Organization:  NCBS Bangalore
+ *        License:  MIT License
+ */
+
+#ifndef MOOSEPARSER_H
+#define MOOSEPARSER_H
+
+#include "../external/muparser/include/muParser.h"
+
+class MooseParser : public mu::Parser
+{
+    public:
+        MooseParser();
+        ~MooseParser();
+
+    private:
+        /* data */
+};
+
+#endif /* end of include guard: MOOSEPARSER_H */
diff --git a/external/muparser/include/muParser.h b/external/muparser/include/muParser.h
@@ -107,7 +107,8 @@ namespace mu
     static value_type  Rand2(value_type, value_type, value_type);
 
      // Random number between 0 and 1, non-deterministic seed.
-    static value_type  Rand( value_type  );
+    static value_type  Rand( value_type seed );
+    static value_type  Rnd( );
 
     // Prefix operators
     // !!! Unary Minus is a MUST if you want to use negative signs !!!

diff --git a/external/muparser/src/muParser.cpp b/external/muparser/src/muParser.cpp
@@ -25,6 +25,7 @@
 */
 #include "../include/muParser.h"
 #include "../include/muParserTemplateMagic.h"
+#include "../../../basecode/global.h"
 
 //--- Standard includes ------------------------------------------------------------------------
 #include <cmath>
@@ -112,10 +113,24 @@ namespace mu
   value_type Parser::Fmod(value_type v1, value_type v2) { return fmod(v1, v2); }
   value_type Parser::Quot(value_type v1, value_type v2) { return (int)(v1 / v2); }
 
+  value_type Parser::Rand( value_type seed = -1 )
+  {
+      static bool isSeedSet_ = false;
+
+      if( ! isSeedSet_ )
+      {
+          mu::rng.setSeed( seed );
+          isSeedSet_ = true;
+      }
+      return rng.uniform( );                    /* Between 0 and 1 */
+  }
+
   // If no seed is given,
-  value_type Parser::Rand( value_type seed )
+  value_type Parser::Rnd( )
   {
       static bool isSeedSet_ = false;
+      // check if global seed is set
+      size_t seed = moose::getGlobalSeed();
       if( ! isSeedSet_ )
       {
           mu::rng.setSeed( seed );
@@ -330,6 +345,7 @@ namespace mu
       DefineFun(_T("rint"), Rint);
       DefineFun(_T("abs"), Abs);
       DefineFun(_T("fmod"), Fmod);
+      DefineFun(_T("rnd"), Rnd);
       DefineFun(_T("rand"), Rand);
       DefineFun(_T("rand2"), Rand2);
       // Functions with variable number of arguments

diff --git a/ksolve/FuncTerm.h b/ksolve/FuncTerm.h
@@ -10,7 +10,7 @@
 #ifndef _FUNC_TERM_H
 #define _FUNC_TERM_H
 
-#include "../external/muparser/include/muParser.h"
+#include "../builtins/MooseParser.h"
 
 class FuncTerm
 {
@@ -44,7 +44,7 @@ class FuncTerm
         double* args_;
         // Look up reactants in the S vec.
         vector< unsigned int > reactantIndex_;
-        mu::Parser parser_;
+        MooseParser parser_;
         string expr_;
         /**
          * Scale factor to account for pool volume if we are assigning conc