Added mmsp2csv and mmsp2txt

examples/Integration_with_fftw/Makefile

@@ -0,0 +1,69 @@
+# Makefile
+
+# includes
+MMSP_PATH=/home/arun/mmsp
+incdir = $(MMSP_PATH)/include
+utildir = $(MMSP_PATH)/utility
+algodir = $(MMSP_PATH)/algorithms
+
+# compilers/flags
+compiler = g++ -std=c++11 -O3 
+pcompiler = mpic++ -std=c++11 -O3 -Wall -pedantic
+flags = -I$(incdir) -I$(algodir) -I$(utildir) 
+prefourierflags = -I fftw/api -fopenmp 
+postfourierflags = fftw/fftw++.cc  
+fourierlinkers = -lfftw3 -lfftw3_omp -lm
+
+
+
+# IBM compiler for AMOS
+BG_XL = /bgsys/drivers/ppcfloor/comm/xl
+BG_INC = -I$(BG_XL)/include
+BG_LIB = -L$(BG_XL)/lib
+qcompiler = $(BG_XL)/bin/mpixlcxx_r -O3 -qflag=w -qstrict -qmaxmem=-1
+qflags = $(BG_INC) $(BG_LIB) $(flags) -I/bgsys/apps/CCNI/zlib/zlib-1.2.7/include -L/bgsys/apps/CCNI/zlib/zlib-1.2.7/lib
+
+# dependencies
+core = #$Thermo.hpp \
+       #$(incdir)/MMSP.main.hpp \
+       $(incdir)/MMSP.utility.h \
+       $(incdir)/MMSP.grid.h \
+       $(incdir)/MMSP.sparse.h \
+
+# the program
+sparse: $(core)
+	$(compiler) $(flags) $(prefourierflags) main.cpp  $(postfourierflags) $(fourierlinkers) $< -o sparse.out -lz  #-include mpi.h
+
+parallel: $(core)
+	$(pcompiler) $(flags) main_parallel.cpp $< -o parallel.out -lz  #-include mpi.h
+
+sparse_serial: $(core)
+	$(compiler) $(flags) $(prefourierflags)  main.cpp $(postfourierflags) $(fourierlinkers)  $< -o sparse_serial.out -lz #
+
+bgq: sp-xmpf.cpp $(core)
+	$(qcompiler) -DBGQ $(qflags) $< -o q_sparse.out -lz
+
+tool: tool.cpp $(core) /usr/include/IL/devil_cpp_wrapper.hpp
+	$(pcompiler) $(flags) -I /usr/include/IL -include il.h $< -o $@ -lz -lIL -lILU -lILUT
+
+mmsp2png : mmsp2png.cpp
+	$(compiler) $(flags) $< -o $@ -lz -lpng
+
+# convert MMSP grid file to ParaView Data file type
+mmsp2pvd : mmsp2pvd.cpp
+	$(compiler) $(flags) $< -o $@ -lz
+
+# convert MMSP grid file to tab-delimited ASCII (TSV) file type
+mmsp2tsv : mmsp2tsv.cpp
+	$(compiler) $(flags) $< -o $@ -lz
+
+# convert MMSP grid file to VTK Image file type
+mmsp2vti : mmsp2vti.cpp
+	$(compiler) $(flags) $< -o $@ -lz
+
+# convert MMSP grid file to XYZ point cloud file type
+mmsp2xyz : mmsp2xyz.cpp
+	$(compiler) $(flags) $< -o $@ -lz
+
+clean:
+	rm -rf sparse.out output_* pf_* delta* c_* IE* *~

examples/Integration_with_fftw/Thermo.hpp

@@ -0,0 +1,206 @@
+#define L0_BCC_Al_Ti_V (32045.963)   
+#define L1_BCC_Al_Ti_V 0.0 //(-113926.0 + 40*T) 
+#define L2_BCC_Al_Ti_V 0.0 //(75972.5 - 150*T) 
+#define L0_HCP_Al_Ti_V 0.0 
+#define L1_HCP_Al_Ti_V 0.0 //(-206074.0 - 40*T) 
+#define L2_HCP_Al_Ti_V 0 
+#define L0_BCC_Ti_V (10500-1.5*T) 
+#define L1_BCC_Ti_V 0.0 //2025.39 
+#define L2_BCC_Ti_V 0.0 
+#define L0_HCP_Ti_V 20000.0
+#define L1_HCP_Ti_V 0.0
+#define L2_HCP_Ti_V 0.0
+#define L0_BCC_Al_Ti (-125980.0+39*T)
+#define L1_BCC_Al_Ti 0.0 //4890.0 
+#define L2_BCC_Al_Ti 0.0 //400.0 
+#define L0_HCP_Al_Ti (-128664.0+37.863*T)
+#define L1_HCP_Al_Ti 0.0 //(-3475.0 + 0.825*T) 
+#define L2_HCP_Al_Ti 0.0 //-7756.0 
+#define L0_HCP_Al_V (-95000.0+20*T)
+#define L1_HCP_Al_V 0.0
+#define L2_HCP_Al_V 0.0
+#define L0_BCC_Al_V (-95000.0+20*T)
+#define L1_BCC_Al_V 0.0 //6645.0 
+#define L2_BCC_Al_V 0.0 //-68596.0 
+
+#define Al_alpha_a_1 -2495.15 
+#define Al_alpha_b_1 135.29 
+#define Al_alpha_c_1 -24.37 
+#define Al_alpha_d_1 -0.00188 
+
+#define Al_alpha_a_2 -5795.24 
+#define Al_alpha_b_2 221.25 
+#define Al_alpha_c_2 -38.58 
+#define Al_alpha_d_2 -0.01853 
+
+#define Al_alpha_a_3 -5797.36 
+#define Al_alpha_b_3 186.88 
+#define Al_alpha_c_3 -31.75 
+#define Al_alpha_d_3 0.0 
+
+#define Al_beta_a_1 2106.85 
+#define Al_beta_b_1 132.28 
+#define Al_beta_c_1 -24.37 
+#define Al_beta_d_1 -0.00188 
+
+#define Al_beta_a_2 -1193.24 
+#define Al_beta_b_2 218.24 
+#define Al_beta_c_2 -38.58 
+#define Al_beta_d_2 -0.01853 
+
+#define Al_beta_a_3 -1195.36 
+#define Al_beta_b_3 183.87 
+#define Al_beta_c_3 -31.75 
+#define Al_beta_d_3 0.0 
+
+#define Ti_alpha_a_1 -8059.92 
+#define Ti_alpha_b_1 133.62 
+#define Ti_alpha_c_1 -23.99 
+#define Ti_alpha_d_1 -0.00477 
+
+#define Ti_alpha_a_2 -7811.82 
+#define Ti_alpha_b_2 132.98 
+#define Ti_alpha_c_2 -23.98 
+#define Ti_alpha_d_2 -0.0042 
+
+#define Ti_alpha_a_3 908.84   
+#define Ti_alpha_b_3 66.98 
+#define Ti_alpha_c_3 -14.95 
+#define Ti_alpha_d_3 -0.00815 
+
+#define Ti_alpha_a_4 -124526.79   
+#define Ti_alpha_b_4 638.81 
+#define Ti_alpha_c_4 -87.22 
+#define Ti_alpha_d_4 -0.00821 
+
+#define Ti_beta_a_1 -1272.06 
+#define Ti_beta_b_1 134.71 
+#define Ti_beta_c_1 -25.58 
+#define Ti_beta_d_1 -0.00066 
+
+#define Ti_beta_a_2 6667.39 
+#define Ti_beta_b_2 105.37 
+#define Ti_beta_c_2 -22.37 
+#define Ti_beta_d_2 0.00122 
+
+#define Ti_beta_a_3 26483.26 
+#define Ti_beta_b_3 -182.43 
+#define Ti_beta_c_3 19.09 
+#define Ti_beta_d_3 -22.01 
+
+
+#define V_alpha_a_1 -3930.43 
+#define V_alpha_b_1 135.74  
+#define V_alpha_c_1 -24.13 
+#define V_alpha_d_1 -0.0031 
+
+#define V_alpha_a_2 -3967.84 
+#define V_alpha_b_2 145.69 
+#define V_alpha_c_2 -25.90 
+#define V_alpha_d_2 0.000063 
+
+#define V_alpha_a_3 -37689.86 
+#define V_alpha_b_3 323.54 
+#define V_alpha_c_3 -47.43 
+#define V_alpha_d_3 0.0 
+
+#define V_beta_a_1 -7930.43 
+#define V_beta_b_1 133.35 
+#define V_beta_c_1 -24.13 
+#define V_beta_d_1 -0.0031 
+
+#define V_beta_a_2 -7967.84 
+#define V_beta_b_2 143.29 
+#define V_beta_c_2 -25.90 
+#define V_beta_d_2 0.000063 
+
+#define V_beta_a_3 -41689.87 
+#define V_beta_b_3 321.14 
+#define V_beta_c_3 -47.43 
+#define V_beta_d_3 0.0 
+
+
+#define q_alpha_al_al -79800 + R*T*log(2.38e-05)
+#define q_alpha_al_v -258550 + R*T*log(4.36e-02)
+#define q_alpha_al_ti -193200 + R*T*log(1.0e-08)
+#define q_alpha_v_al -79800 + R*T*log(2.38e-05)
+#define q_alpha_v_v -258550 + R*T*log(4.36e-02)
+#define q_alpha_v_ti -251490 -56*T
+
+#define a_alpha_al_al_ti -491950
+#define a_alpha_al_ti_v 587700
+#define a_alpha_al_al_v 0.0
+#define a_alpha_v_al_ti -529600
+#define a_alpha_v_al_v 0.0
+#define a_alpha_v_ti_v 0.0
+
+
+#define q_beta_al_al -215000 -80.2*T
+#define q_beta_al_v -268000 -97.2*T
+#define q_beta_al_ti R*T*log(5.19e-10*exp(-96000/(R*T)))
+#define q_beta_v_al -325008.12 -73.99*T
+#define q_beta_v_v -325008.12 -73.99*T
+#define q_beta_v_ti -179392.69 - 106.68*T
+
+#define a_beta_al_al_ti -499946.15 + 333.87*T
+#define a1_beta_al_al_ti -407271.50 + 286.27*T  
+#define a_beta_al_al_v -751405.09
+#define a_beta_al_ti_v 0.0
+#define a_beta_v_al_v -1300707.37
+#define a_beta_v_ti_v +159597.07 - 48.62*T
+#define a1_beta_v_ti_v -10551.39
+#define a_beta_v_al_ti 0.0
+
+void thermo_auxillary_terms(MMSP::vector<store_type> gradient, MMSP::vector<store_type> gradientsq, double c_Al, double c_V)
+{
+	double grad_cal = 0 ;
+	double grad_cv = 0 ;
+	double gradsq_cal = 0 ;
+	double gradsq_cv = 0 ;
+	for(int i = 0; i < dim ; i++)
+	{
+		grad_cal += gradient[i][20] ;
+		grad_cv += gradient[i][21]  ;
+		gradsq_cal += gradientsq[i][20] ;
+		gradsq_cv += gradientsq[i][21] ;
+	}
+	dGAlpha_dAl = (G_Al_alpha/G_normalize - G_Ti_alpha/G_normalize) + log(c_Al) - log((1-c_Al-c_V)) + c_V*L0_HCP_Al_V/G_normalize + 
+							(1-2*c_Al-c_V)*L0_HCP_Al_Ti/G_normalize - c_V*L0_HCP_Ti_V/G_normalize ;
+	dGBeta_dAl = (G_Al_beta/G_normalize - G_Ti_beta/G_normalize) + log(c_Al) - log((1-c_Al-c_V)) + c_V*L0_BCC_Al_V/G_normalize +
+						    (1-2*c_Al-c_V)*L0_BCC_Al_Ti/G_normalize - c_V*L0_BCC_Ti_V/G_normalize + (c_V*(1-c_Al-c_V)
+						     - c_Al*c_V)*L0_BCC_Al_Ti_V/G_normalize ;
+	dGAlpha_dV = (G_V_alpha/G_normalize - G_Ti_alpha/G_normalize) + log(c_V) - log((1-c_Al-c_V)) + c_Al*L0_HCP_Al_V/G_normalize +
+							(1-c_Al-2*c_V)*L0_HCP_Ti_V/G_normalize - c_Al*L0_HCP_Al_Ti/G_normalize ;	
+	dGBeta_dV = (G_V_beta/G_normalize - G_Ti_beta/G_normalize) + log(c_V) - log((1-c_Al-c_V)) + c_Al*L0_BCC_Al_V/G_normalize +
+							(1-c_Al-2*c_V)*L0_BCC_Ti_V/G_normalize - c_Al*L0_BCC_Al_Ti/G_normalize + (c_Al*(1-c_Al-c_V) -
+							c_Al*c_V)*L0_BCC_Al_Ti_V/G_normalize ;
+	del_dGAlpha_dAl = grad_cal*(1.0/c_Al + 1.0/(1.0-c_Al-c_V) - 2*L0_HCP_Al_Ti/G_normalize) + grad_cv*(1.0/(1.0-c_Al-c_V) +
+							L0_HCP_Al_V/G_normalize - L0_HCP_Al_Ti/G_normalize -L0_HCP_Ti_V/G_normalize) ;
+	del_dGBeta_dAl = grad_cal*(1.0/c_Al + 1/(1-c_Al-c_V) - 2*L0_BCC_Al_Ti/G_normalize - 2*c_V*L0_BCC_Al_Ti_V/G_normalize) + 
+								grad_cv*(1/(1-c_Al-c_V) + L0_HCP_Al_V/G_normalize - L0_HCP_Al_Ti/G_normalize -L0_HCP_Ti_V/G_normalize +
+								(1-2*c_Al-2*c_V)*L0_BCC_Al_Ti_V/G_normalize) ;	
+	del_dGAlpha_dV = grad_cv*(1.0/c_V + 1/(1-c_Al-c_V) - 2*L0_HCP_Ti_V/G_normalize) + grad_cal*(1/(1-c_Al-c_V) + 
+						    L0_HCP_Al_V/G_normalize - L0_HCP_Al_Ti/G_normalize - L0_HCP_Ti_V/G_normalize) ;	
+	del_dGBeta_dV = 	grad_cv*(1.0/c_V + 1/(1-c_Al-c_V) -2*L0_BCC_Ti_V/G_normalize - 2*c_Al*L0_BCC_Al_Ti_V/G_normalize) + 
+							    grad_cal*(1/(1-c_Al-c_V) + L0_BCC_Al_V/G_normalize - L0_BCC_Al_Ti/G_normalize - L0_BCC_Ti_V/G_normalize + 
+							    (1-2*c_Al-2*c_V)*L0_BCC_Al_Ti_V/G_normalize) ;										    
+	delsq_dGAlpha_dAl = gradsq_cal*(1.0/c_Al + 1/(1-c_Al-c_V) - 2*L0_HCP_Al_Ti/G_normalize) + gradsq_cv*(1/(1-c_Al-c_V) +
+								L0_HCP_Al_V/G_normalize - L0_HCP_Al_Ti/G_normalize -L0_HCP_Ti_V/G_normalize) + grad_cal*(-grad_cal/pow(c_Al,2) +
+								(grad_cal + grad_cv)/pow((1-c_Al-c_V),2)) + grad_cv*((grad_cal + grad_cv)/pow((1-c_Al-c_V),2)) ;
+
+	delsq_dGAlpha_dV = gradsq_cv*(1.0/c_V + 1/(1-c_Al-c_V) - 2*L0_HCP_Ti_V/G_normalize) + gradsq_cal*(1/(1-c_Al-c_V) +
+									L0_HCP_Al_V/G_normalize - L0_HCP_Al_Ti/G_normalize - L0_HCP_Ti_V/G_normalize) + grad_cv*(-grad_cv/pow(c_V,2) +
+									(grad_cal + grad_cv)/pow((1-c_Al-c_V),2)) + grad_cal*((grad_cal + grad_cv)/pow((1-c_Al-c_V),2)) ;					
+
+	delsq_dGBeta_dAl = gradsq_cal*(1.0/c_Al + 1/(1-c_Al-c_V) - 2*L0_BCC_Al_Ti/G_normalize - 2*c_V*L0_BCC_Al_Ti_V/G_normalize) +
+								  gradsq_cv*(1/(1-c_Al-c_V) + L0_HCP_Al_V/G_normalize - L0_HCP_Al_Ti/G_normalize -L0_HCP_Ti_V/G_normalize +
+								   (1-2*c_Al-2*c_V)*L0_BCC_Al_Ti_V/G_normalize) + grad_cal*(-grad_cal/pow(c_Al,2) + (grad_cal +
+								    grad_cv)/pow((1-c_Al-c_V),2) - 2*grad_cv*L0_BCC_Al_Ti_V/G_normalize) + grad_cv*((grad_cal +
+								     grad_cv)/pow((1-c_Al-c_V),2) + (-2*grad_cal*grad_cv)*L0_BCC_Al_Ti_V/G_normalize) ;							
+	delsq_dGBeta_dV = gradsq_cv*(1.0/c_V + 1/(1-c_Al-c_V) -2*L0_BCC_Ti_V/G_normalize - 2*c_Al*L0_BCC_Al_Ti_V/G_normalize) +
+								 gradsq_cal*(1/(1-c_Al-c_V) + L0_BCC_Al_V/G_normalize - L0_BCC_Al_Ti/G_normalize - L0_BCC_Ti_V/G_normalize + 
+								(1-2*c_Al-2*c_V)*L0_BCC_Al_Ti_V/G_normalize) + grad_cv*(-grad_cv/pow(c_V,2) + (grad_cal + 
+								grad_cv)/pow((1-c_Al-c_V),2) - 2*grad_cal*L0_BCC_Al_Ti_V/G_normalize) + grad_cal*((grad_cal + 
+								grad_cv)/pow((1-c_Al-c_V),2) + (-2*grad_cal*grad_cv)*L0_BCC_Al_Ti_V/G_normalize) ;
+}
+