quantum-kite · ngaro · Nov 9, 2019 · Nov 9, 2019 · Nov 9, 2019 · Nov 9, 2019
diff --git a/Dockerfile.buildenv b/Dockerfile.buildenv
@@ -10,6 +10,7 @@ RUN apt-get -y install valgrind gdb strace
 RUN apt-get -y install libhdf5-dev libeigen3-dev
 
 RUN groupadd -g $GID -o $UNAME && useradd -m -u $UID -g $GID -o -s /bin/bash $UNAME
+RUN chown $UNAME /usr/local/bin
 
 USER $UNAME
 RUN mkdir /home/${UNAME}/kite

diff --git a/tools/src/arpes.cpp b/tools/src/arpes.cpp
@@ -366,15 +366,15 @@ void arpes<U, DIM>::calculate(){
   if(calculate_full_arpes){
 
     Eigen::Matrix<double, -1, -1> incidents = Eigen::Matrix<double, -1, -1>::Zero(DIM, NumVectors);
-    for(int ii = 0; ii < NumVectors; ii++){
+    for(unsigned int ii = 0; ii < NumVectors; ii++){
       incidents.col(ii) = incident_vector;
     }
 
     Eigen::Matrix<double, -1, -1> modulation = Eigen::Matrix<double, -1, -1>::Zero(1, NumVectors);
     modulation = incident_vector.matrix().transpose()*(incidents + arpes_k_vectors.matrix())/incident_vector.matrix().norm();
 
 
-    for(int ii = 0; ii < NumVectors; ii++){
+    for(unsigned int ii = 0; ii < NumVectors; ii++){
       ARPES.col(ii) *= modulation(ii)*modulation(ii);
     }
   }

diff --git a/tools/src/cond_2order/Gamma1.cpp b/tools/src/cond_2order/Gamma1.cpp
@@ -37,7 +37,7 @@ Eigen::Matrix<std::complex<U>, -1, -1> conductivity_nonlinear<U, DIM>::Gamma1shg
   int thread_num;
   int local_NumMoments;
   omp_set_num_threads(systemInfo.NumThreads);
-#pragma omp parallel shared(N_threads, cond) firstprivate(thread_num, DeltaMatrix)
+#pragma omp parallel shared(N_threads, cond) firstprivate(DeltaMatrix) private(thread_num)
 {
 #pragma omp master
 {

diff --git a/tools/src/cond_2order/Gamma1photo.cpp b/tools/src/cond_2order/Gamma1photo.cpp
@@ -42,7 +42,7 @@ Eigen::Matrix<std::complex<U>, -1, -1> conductivity_nonlinear<U, DIM>::Gamma1con
   int local_NumMoments;
 
   omp_set_num_threads(systemInfo.NumThreads);
-#pragma omp parallel shared(N_threads, cond) firstprivate(thread_num, DeltaMatrix)
+#pragma omp parallel shared(N_threads, cond) firstprivate(DeltaMatrix) private(thread_num)
 {
 #pragma omp master
 {

diff --git a/tools/src/cond_2order/Gamma2.cpp b/tools/src/cond_2order/Gamma2.cpp
@@ -38,7 +38,7 @@ Eigen::Matrix<std::complex<U>, -1, -1> conductivity_nonlinear<U, DIM>::Gamma2shg
   int thread_num;
   int local_NumMoments;
   omp_set_num_threads(systemInfo.NumThreads);
-#pragma omp parallel shared(N_threads, cond) firstprivate(thread_num, DeltaMatrix)
+#pragma omp parallel shared(N_threads, cond) firstprivate(DeltaMatrix) private(thread_num)
 {
 #pragma omp master
 {
@@ -72,11 +72,21 @@ Eigen::Matrix<std::complex<U>, -1, -1> conductivity_nonlinear<U, DIM>::Gamma2shg
     local_cond = Eigen::Matrix<std::complex<U>, -1, -1>::Zero(N_energies, N_omegas);
 
     // Loop over the frequencies
-    //U w1, w2;
-    U w1, w2;
+/*
+ * Although frequencies2(w,0) was used to set w1 this value is never being used again.
+ * So i removed w1 from the code. To make sure that the program works exactly the same
+ * I still run frequencies2(w,0). This is needed because this function might do some
+ * things that influence other data, generate output, ...
+ *
+ * I assume that not using w1 was an oversight. If this is true I suggest uncommenting the
+ * code again and actually using it.
+ *
+ * -- Nikolas Garofil
+ */
+    U /*w1,*/ w2;
     std::complex<U> GammaEp, GammaEn, GammaE;
     for(int w = 0; w < N_omegas; w++){
-      w1 = frequencies2(w,0);
+      /*w1 = */frequencies2(w,0);
       w2 = frequencies2(w,1);
 
       for(int e = 0; e < N_energies; e++){

diff --git a/tools/src/cond_2order/Gamma2photo.cpp b/tools/src/cond_2order/Gamma2photo.cpp
@@ -37,7 +37,7 @@ Eigen::Matrix<std::complex<U>, -1, -1> conductivity_nonlinear<U, DIM>::Gamma2con
   int thread_num;
   int local_NumMoments;
   omp_set_num_threads(systemInfo.NumThreads);
-#pragma omp parallel shared(N_threads, cond) firstprivate(thread_num, DeltaMatrix)
+#pragma omp parallel shared(N_threads, cond) firstprivate(DeltaMatrix) private(thread_num)
 {
 #pragma omp master
 {

diff --git a/tools/src/cond_2order/Gamma3.cpp b/tools/src/cond_2order/Gamma3.cpp
@@ -32,7 +32,6 @@ Eigen::Matrix<std::complex<U>, -1, -1> conductivity_nonlinear<U, DIM>::Gamma3shg
   // number of threads, thread number and number of moments alocated
   // to each thread. These have to be computed inside a threaded block
   int N_threads;
-  int thread_num;
   int local_NumMoments;
 
   // Functions that are going to be used by the contractor
@@ -143,7 +142,6 @@ Eigen::Matrix<std::complex<U>, -1, -1> conductivity_nonlinear<U, DIM>::Gamma3shg
   // number of threads, thread number and number of moments alocated
   // to each thread. These have to be computed inside a threaded block
   int N_threads;
-  int thread_num;
   int local_NumMoments;
 
   // Functions that are going to be used by the contractor
@@ -256,7 +254,6 @@ Eigen::Matrix<std::complex<U>, -1, -1> conductivity_nonlinear<U, DIM>::Gamma3shg
   // number of threads, thread number and number of moments alocated
   // to each thread. These have to be computed inside a threaded block
   int N_threads;
-  int thread_num;
   int local_NumMoments;
 
   // Functions that are going to be used by the contractor

diff --git a/tools/src/cond_2order/Gamma3photo.cpp b/tools/src/cond_2order/Gamma3photo.cpp
@@ -154,7 +154,6 @@ Eigen::Matrix<std::complex<U>, -1, -1> conductivity_nonlinear<U, DIM>::Gamma3Con
   // number of threads, thread number and number of moments alocated
   // to each thread. These have to be computed inside a threaded block
   int N_threads;
-  int thread_num;
   int local_NumMoments;
 
   // Functions that are going to be used by the contractor

diff --git a/tools/src/cond_2order/conductivity_2order.cpp b/tools/src/cond_2order/conductivity_2order.cpp
@@ -155,7 +155,6 @@ conductivity_nonlinear<T, DIM>::conductivity_nonlinear(system_info<T, DIM>& info
     // KPM parameters
     NumPoints = -1;
     special = 0;
-    dirString; 
 
   std::string name = info.filename;                           // name of the hdf5 file
   file = H5::H5File(name.c_str(), H5F_ACC_RDONLY);
@@ -347,11 +346,22 @@ void conductivity_nonlinear<U, DIM>::calculate_photo(){
   }
 
   U freq;
-  U w1, w2;
+/*
+ * Although frequencies2() was used to set w1 and w2 these values are never being used again.
+ * So i removed w1 and w2 from the code. To make sure that the program works exactly the same
+ * I still run the frequencies2() functions. This is needed because this function might do some
+ * things that influence other data, generate output, ...
+ *
+ * I assume that not using w1 and w2 was an oversight. If this is true I suggest uncommenting the
+ * code again and actually using it.
+ *
+ * -- Nikolas Garofil
+ */
+  //U w1, w2;
   for(int w = 0; w < N_omegas; w++){
     freq = frequencies(w);  
-    w1 = frequencies2(w,0);
-    w2 = frequencies2(w,1);
+    /*w1 =*/ frequencies2(w,0);
+    /*w2 =*/ frequencies2(w,1);
 
     // Energy integration
     cond0(w) = integrate(energies, Eigen::Matrix<std::complex<U>,-1,1>(omega_energies0.col(w)));

diff --git a/tools/src/cond_dc/conductivity_dc.cpp b/tools/src/cond_dc/conductivity_dc.cpp
@@ -375,7 +375,7 @@ void conductivity_dc<U, DIM>::calculate2(){
 
   // save to a file
   save_to_file(condDC);
-};
+}
 
 
 // Instantiations

diff --git a/tools/src/macros.hpp b/tools/src/macros.hpp
@@ -1,5 +1,5 @@
-#define outcol "\033[1;31m"
-#define outres "\033[0m"
+#define TEXTCOLOR_RED "\033[1;31m"
+#define TEXTCOLOR_RESET "\033[0m"
 
 #ifndef DEBUG
 #define DEBUG 1
@@ -9,29 +9,22 @@
 #define VERBOSE 1
 #endif
 
+#define PI 3.14159265
 // The first scale is 1/2pi and corresponds to the conductance quantum per spin e^2/h
 // The second scale is the universal conductivity of graphene e^2/4h_bar
-#define scale1 0.159154943
+#define scale1 1/(2*PI)
 #define scale2 0.25
-#define unit_scale 0.159154943
+#define unit_scale 1/(2*PI)
 
-#ifdef VERBOSE
-	#if VERBOSE==1
-		#define verbose_message(VAR) std::cout<<VAR<<std::flush
-	#else
-		#define verbose_message(VAR) 
-	#endif
+#if VERBOSE==1
+	#define verbose_message(VAR) std::cout<<VAR<<std::flush
 #else
 	#define verbose_message(VAR) 
 #endif
 
-#ifdef DEBUG
-	#if DEBUG==1
-		#define debug_message(VAR) std::cout << outcol << VAR << outres << std::flush
-		#define verbose_message(VAR) std::cout<<VAR<<std::flush
-	#else
-		#define debug_message(VAR) 
-	#endif
+#if DEBUG==1
+	#define debug_message(VAR) std::cout << TEXTCOLOR_RED << VAR << TEXTCOLOR_RESET << std::flush
+	#define verbose_message(VAR) std::cout<<VAR<<std::flush
 #else
 	#define debug_message(VAR) 
 #endif
diff --git a/tools/src/main.cpp b/tools/src/main.cpp
@@ -21,10 +21,6 @@
 #include "compiletime_info.h"
 
 int main(int argc, char *argv[]){
-  if(argc < 2){
-    std::cout << "No configuration file found. Exiting.\n";
-    exit(1);
-  }
   shell_input variables(argc, argv);
   print_header_message();
   print_info_message();

diff --git a/tools/src/messages.hpp b/tools/src/messages.hpp
@@ -1,53 +1,59 @@
 void print_header_message(){
 #if VERBOSE
-    std::cout << 
-      "\n+------------------------------------------------------------------------+\n"
-      "|            Chebyshev Polynomial Green's Function Approach              | \n"
-      "|             to Real-Space Quantum Transport Simulations                | \n"    
-      "|                                                                        | \n"                                              
-      "|                     KITE | Release 1.0                                 | \n"         
-      "|                     Kite home: quantum-kite.com                        | \n"
-      "|                                                                        | \n"
-      "|    Created by Simao M. Joao, Joao V. Lopes (Universidade do Porto),    | \n"
-      "|      Tatiana G. Rappoport (Universidade Federal Rio de Janeiro),       | \n"
-      "|        Misa Andelkovic, Lucian Covaci (University of Antwerp)          | \n"
-      "|                and Aires Ferreira (University of York)                 | \n"
-      "|                                                                        | \n"                                            
-      "|            Funded by The Royal Society | royalsociety.org              | \n"
-      "|                                                                        | \n"
-      "|  Copyright (C) 2018, 2109, M. Andelkovic, L. Covaci, A. Ferreira,      | \n"
-      "|                      S. M. Joao, J. V. Lopes, T. G. Rappoport          | \n"
-      "|                                                                        | \n"
-      "|  This program is free software: you can redistribute it and/or modify  | \n"
-      "|  it under the terms of the GNU General Public License as published by  | \n"
-      "|  the Free Software Foundation, either version 3 of the License, or     | \n"
-      "|  (at your option) any later version.                                   | \n"
-      "|                                                                        | \n"
-      "|  This program is distributed in the hope that it will be useful,       | \n"
-      "|  but WITHOUT ANY WARRANTY; without even the implied warranty of        | \n"
-      "|  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.                  | \n"
-      "|  See the GNU General Public License for more details.                  | \n"
-      "+------------------------------------------------------------------------+\n";
+    std::cout << R"ENDSTRING(
+
++------------------------------------------------------------------------+
+|            Chebyshev Polynomial Green's Function Approach              |
+|             to Real-Space Quantum Transport Simulations                |
+|                                                                        |
+|                     KITE | Release 1.0                                 |
+|                     Kite home: quantum-kite.com                        |
+|                                                                        |
+|    Created by Simao M. Joao, Joao V. Lopes (Universidade do Porto),    |
+|      Tatiana G. Rappoport (Universidade Federal Rio de Janeiro),       |
+|        Misa Andelkovic, Lucian Covaci (University of Antwerp)          |
+|                and Aires Ferreira (University of York)                 |
+|                                                                        |
+|            Funded by The Royal Society | royalsociety.org              |
+|                                                                        |
+|  Copyright (C) 2018, 2019, M. Andelkovic, L. Covaci, A. Ferreira,      |
+|                      S. M. Joao, J. V. Lopes, T. G. Rappoport          |
+|                                                                        |
+|  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 of the License, 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.                  |
++------------------------------------------------------------------------+
+)ENDSTRING";
 #endif
 }
 
 void print_flags_message(){
 #if VERBOSE
     std::cout <<
-        "------- FLAGS SET -------\n"
-        "DEBUG: "     << DEBUG    <<"\n"
-        "VERBOSE: "   << VERBOSE  << "\n"
-        "-------------------------\n\n";
+        "------- FLAGS SET -------" << std::endl <<
+        "DEBUG: "     << DEBUG    << std::endl <<
+        "VERBOSE: "   << VERBOSE  <<  std::endl <<
+        "-------------------------" << std::endl <<
+	"" <<std::endl;
 #endif
 }
 
 void print_info_message(){
 #if VERBOSE
-    std::cout << 
-        "\n------------------------------ INFORMATION ------------------------------\n"
-        "Linear response functions in units of e^2/h.                              \n"
-        "To stop these messages, set VERBOSE to 0 in the Makefile.                 \n"
-        "To see debug messages, set DEBUG to 1 in the Makefile.                    \n"
-        "------------------------------------------------------------------------- \n\n";
+    std::cout << R"ENDSTRING(
+
+------------------------------ INFORMATION ------------------------------
+Linear response functions in units of e^2/h.
+To stop these messages, set VERBOSE to 0 in the Makefile.
+To see debug messages, set DEBUG to 1 in the Makefile.
+-------------------------------------------------------------------------
+
+)ENDSTRING";
 #endif
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -375,7 +375,7 @@ void conductivity_dc<U, DIM>::calculate2(){ @@
       // save to a file
       save_to_file(condDC);
-    };
+    }
     // Instantiations
@@ Expand Down @@