Merge branch 'develop' of github.com:ttadano/alamode into develop

ttadano · Sep 19, 2018 · 241009f · 241009f
2 parents 0eafea5 + 5a9b69c
commit 241009f
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Showing 63 changed files with 5,349 additions and 3,864 deletions.
diff --git a/alm/Makefile.osx b/alm/Makefile.osx
@@ -7,7 +7,7 @@
 
 # Use gcc >= 4.8 to use OpenMP 
 # OpenMP-enabled gcc can be installed via homebrew
-CXX = g++-7
+CXX = g++-8
 CXXFLAGS = -O2 -fopenmp -std=c++11
 INCLUDE = -I../include
 

diff --git a/alm/constraint.cpp b/alm/constraint.cpp
@@ -196,11 +196,21 @@ void Constraint::setup()
             nparam = fcs->nequiv[order].size();
             memory->allocate(arr_tmp, nparam);
 
+            if (const_symmetry[order].size() > 0) {
+                for (it_const = const_symmetry[order].begin();
+                     it_const != const_symmetry[order].end(); ++it_const) {
+                    for (i = 0; i < nparam; ++i) arr_tmp[i] = (*it_const).w_const[i];
+                    const_self[order].push_back(ConstraintClass(nparam, arr_tmp));
+                }
+//                remove_redundant_rows(nparam, const_self[order], eps8);
+            }
+
             for (it_const = const_translation[order].begin();
                  it_const != const_translation[order].end(); ++it_const) {
                 for (i = 0; i < nparam; ++i) arr_tmp[i] = (*it_const).w_const[i];
                 const_self[order].push_back(ConstraintClass(nparam, arr_tmp));
             }
+            remove_redundant_rows(nparam, const_self[order], eps8);
 
             if (const_rotation_self[order].size() > 0) {
                 for (it_const = const_rotation_self[order].begin();
@@ -211,15 +221,6 @@ void Constraint::setup()
                 remove_redundant_rows(nparam, const_self[order], eps8);
             }
 
-            if (const_symmetry[order].size() > 0) {
-                for (it_const = const_symmetry[order].begin();
-                     it_const != const_symmetry[order].end(); ++it_const) {
-                    for (i = 0; i < nparam; ++i) arr_tmp[i] = (*it_const).w_const[i];
-                    const_self[order].push_back(ConstraintClass(nparam, arr_tmp));
-                }
-                remove_redundant_rows(nparam, const_self[order], eps8);
-            }
-
             memory->deallocate(arr_tmp);
             const_translation[order].clear();
             const_rotation_self[order].clear();
@@ -1724,7 +1725,7 @@ void Constraint::rref(int nrows,
 
         if (icol == ncols) break;
 
-        if (std::abs(mat[pivot][icol]) > tolerance) ++nrank;
+        if (std::abs(mat[pivot][icol]) >= tolerance) ++nrank;
 
         if (pivot != irow) {
             //#pragma omp parallel for private(tmp)

diff --git a/anphon/Makefile.linux b/anphon/Makefile.linux
@@ -26,8 +26,8 @@ PROG = anphon
 
 CXXSRC= phonons.cpp error.cpp fcs_phonon.cpp parsephon.cpp dynamical.cpp  \
 	main.cpp memory.cpp system.cpp timer.cpp write_phonons.cpp kpoint.cpp \
-	phonon_dos.cpp phonon_velocity.cpp integration.cpp relaxation.cpp \
-	thermodynamics.cpp conductivity.cpp symmetry_core.cpp \
+	phonon_dos.cpp phonon_velocity.cpp integration.cpp anharmonic_core.cpp \
+	thermodynamics.cpp conductivity.cpp symmetry_core.cpp mode_analysis.cpp \
         mpi_common.cpp gruneisen.cpp isotope.cpp selfenergy.cpp \
 	scph.cpp ewald.cpp
 

diff --git a/anphon/Makefile.osx b/anphon/Makefile.osx
@@ -6,7 +6,7 @@
 #-----------------------------------------------
 
 MPICXX = mpic++
-CXXFLAGS = -O3 -std=c++11
+CXXFLAGS = -O3 -std=c++11 -fopenmp
 INCLUDE = -I../include  -I$(HOME)/include
 
 LINKER = ${MPICXX}
@@ -30,8 +30,8 @@ PROG = anphon
 
 CXXSRC= phonons.cpp error.cpp fcs_phonon.cpp parsephon.cpp dynamical.cpp  \
 	main.cpp memory.cpp system.cpp timer.cpp write_phonons.cpp kpoint.cpp \
-	phonon_dos.cpp phonon_velocity.cpp integration.cpp relaxation.cpp \
-	thermodynamics.cpp conductivity.cpp symmetry_core.cpp \
+	phonon_dos.cpp phonon_velocity.cpp integration.cpp anharmonic_core.cpp \
+	thermodynamics.cpp conductivity.cpp symmetry_core.cpp mode_analysis.cpp \
         mpi_common.cpp gruneisen.cpp isotope.cpp selfenergy.cpp \
 	scph.cpp ewald.cpp
 

diff --git a/anphon/Makefile.osx_gcc b/anphon/Makefile.osx_gcc
@@ -0,0 +1,55 @@
+.SUFFIXES: .h .cpp
+#-----------------------------------------------
+# Makefile for the program 'ANPHON'.
+# Please modify the variables properly.
+# We recommend to use Intel c++ compiler.
+#-----------------------------------------------
+
+MPICXX = g++-8
+CXXFLAGS = -O3 -std=c++11 -fopenmp
+INCLUDE = -I../include  -I$(HOME)/include -I/usr/local/opt/openmpi/include
+
+LINKER = ${MPICXX}
+
+## Mavericks
+#LDFLAGS = -framework vecLib
+## Yosemite
+LDFLAGS = -framework Accelerate
+
+LAPACK = -llapack -L/usr/local/opt/openmpi/lib -lmpi_cxx -lmpi -lgomp
+LIBS = ${LAPACK}  -lfftw3
+
+#----------------------------------------------
+# General rules
+#----------------------------------------------
+
+.cpp.o:
+	${MPICXX} ${CXXFLAGS} ${INCLUDE} -c $<
+
+PROG = anphon
+
+CXXSRC= phonons.cpp error.cpp fcs_phonon.cpp parsephon.cpp dynamical.cpp  \
+	main.cpp memory.cpp system.cpp timer.cpp write_phonons.cpp kpoint.cpp \
+	phonon_dos.cpp phonon_velocity.cpp integration.cpp anharmonic_core.cpp \
+	thermodynamics.cpp conductivity.cpp symmetry_core.cpp mode_analysis.cpp \
+        mpi_common.cpp gruneisen.cpp isotope.cpp selfenergy.cpp \
+	scph.cpp ewald.cpp
+
+OBJS= ${CXXSRC:.cpp=.o}
+
+default: anphon
+
+all: ${PROG}
+
+anphon: ${OBJS}
+	${LINKER} ${LDFLAGS} -o $@ ${OBJS} ${LIBS}
+
+clean:
+	rm -f ${OBJS}
+
+.PHONY: clean
+
+depend:
+	gcc -MM *.cpp > .depend
+
+-include .depend