From 9f4c693d8bd06ca8b0ef35cb00cfdf439b218dc7 Mon Sep 17 00:00:00 2001
From: Dariusz Murakowski <murakdar@mit.edu>
Date: Mon, 27 Jul 2015 17:41:35 -0400
Subject: [PATCH] Add options for separate inverse temperature (beta)
 multipliers for fields and couplings.

---
 mainQEE.cpp      | 2 ++
 qEpitopeEval.cpp | 6 +++++-
 qEpitopeEval.h   | 6 ++++++
 3 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/mainQEE.cpp b/mainQEE.cpp
index 04676cd..fa5a01c 100755
--- a/mainQEE.cpp
+++ b/mainQEE.cpp
@@ -135,6 +135,8 @@ int main(int argc, char *argv[]) {
 
         else if (strcmp(argv[i],"-trackE")==0)   { r.trackE=true;                                                           }
         else if (strcmp(argv[i],"-randInit")==0) { r.randomStart=true;                                                      }
+        else if (strcmp(argv[i],"-betah")==0) { if (++i==argc) break; else r.betah=strtodouble(argv[i]);                    }
+        else if (strcmp(argv[i],"-betaJ")==0) { if (++i==argc) break; else r.betaJ=strtodouble(argv[i]);                    }
         
         else printf("Unrecognized command! '%s'\n",argv[i]);
         
diff --git a/qEpitopeEval.cpp b/qEpitopeEval.cpp
index ba6d3bc..1231a40 100755
--- a/qEpitopeEval.cpp
+++ b/qEpitopeEval.cpp
@@ -34,11 +34,15 @@ void runEpitopeEval(RunParameters &r, std::vector<std::vector<int> > &eStates, s
         
     if (dataIn!=NULL) getCouplings(dataIn,J);
     else { printf("Error reading input from file %s",r.getInfile().c_str()); exit(1); }
-    
+
     // Resize correlations and expJ
     
     int N = sizetolength(J.size());
     
+    // apply temperature multipliers to fields and couplings
+    for (int i=0; i<N; i++) { for (int j=0; j<J[i].size(); j++) { J[i][j] *= r.betah; } }
+    for (int i=N; i<J.size(); i++) { for (int j=0; j<J[i].size(); j++) { J[i][j] *= r.betaJ; } }
+    
     pk.resize(N+1, 0);
     for (int i=0;i<J.size();i++) { p.push_back(std::vector<double>(J[i].size(),0)); expJ.push_back(std::vector<double>(J[i].size(),0)); }
     for (int i=0;i<J.size();i++) { for (int j=0;j<J[i].size();j++) expJ[i][j] = exp(J[i][j]); }
diff --git a/qEpitopeEval.h b/qEpitopeEval.h
index 6ee3345..5a103cf 100755
--- a/qEpitopeEval.h
+++ b/qEpitopeEval.h
@@ -37,6 +37,9 @@ public:
 
     bool trackE;                    // if true, save relative contribution to energy from fields and couplings
     bool randomStart;               // if true, set the initial state randomly
+
+    double betah;                   // inverse temperature multiplier for fields
+    double betaJ;                   // inverse temperature multiplier for couplings
     
     RunParameters() {
         
@@ -55,6 +58,9 @@ public:
 
         trackE = false;
         randomStart = false;
+
+        betah = 1.0;
+        betaJ = 1.0;
         
     }
     std::string getInfile()                   { return (directory+"/"+infile+".j");                   }
-- 
2.7.4