Merge pull request #86 from wszhang/develop

Integrate pytorch+dpsi method into original orbital-generation-script

Author: dyzheng

tools/SIAB/Generate_Orbital_AllInOne.sh

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+# SIAB Package Description
+
+
+(S)ystematically
+(I)mprovable
+(A)tomic orbital
+(B)asis generator based on spillage formula
+
+
+# HOW TO USE SIAB
+
+The optimization can choose three minimization methods: 'Simulated Annealing', 'PyTorch Gradient' and 'PyTorch Gradient whit dpsi'. 
+
+The executable files for three methods are './SimulatedAnnealing/source/SIA_s.exe', './PyTorchGradient/source/main.py', '../opt_orb_pytorch_dpsi/main.py', respectively.
+
+
+##  (1) write input file
+Firstly, write the input file, such as "ORBITAL_INPUT_DZP" in example-directories, for script 'Generate_Orbital_AllInOne.sh'.
+Both approachs, 'PyTorch Gradient' and 'Simulated Annealing', work with one bash script and use the same input file.
+Please use the absolute path for each each file and directory.
+
+
+##  (2) set up dependence env
+Then, we set up the dependence env for ABACUS and SIAB, such as:
+'''
+module load hpcx/2.9.0/hpcx-intel-2019.update5 mkl/2019.update5 elpa/2019.05.002/hpcx-intel-2019.update5
+'''
+Especially for SIAB with 'PyTorch Gradient' approach, we need pytorch v1.1.0.
+
+
+### how to install pytorch:
+Take the HanHai20@USTC system for example:
+
+''' bash
+$ module load gcc/7.5.0min      #:optional, larger version gcc may not be necessary.
+$ module load anaconda3
+$ module list
+Currently Loaded Modulefiles:
+  1) elpa/2019.05.002/hpcx-intel-2019.update5   4) hpcx/2.9.0/hpcx-intel-2019.update5         7) libxc/4.3.4/hpcx-intel-2019.update5
+  2) gcc/7.5.0min                               5) mkl/2019.update5
+  3) intel/2019.update5                         6) anaconda3_nompi
+$ python3 -V
+Python 3.7.4
+
+$ conda create -n pytorch110 python=3.7
+$ source activate pytorch110  #or: conda activate pytorch110
+$ conda install pytorch torchvision torchaudio cpuonly -c pytorch
+$ source deactivate  #or: conda deactivate
+
+$ source activate pytorch110  #or: conda activate pytorch110
+$ pip3 install --user scipy numpy
+$ pip3 install --user torch_optimizer
+'''
+
+
+## (3) run generation
+Finally, 'cd' into an example folder, and run command like this:
+
+''' bash
+../Generate_Orbital_AllInOne.sh ORBITAL_INPUT_DZP
+# or
+bsub -q idle -n 8 -oo running.log ../Generate_Orbital_AllInOne.sh ORBITAL_INPUT_DZP
+'''
+

tools/SIAB/README

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+#===========================================================
+# AUTHOR : mohan
+# DATE START FROM : 2009-04-14
+# FUNCTION : spillage makefile
+#===========================================================
+### Dirac
+#CPLUSPLUS =CC -O3 -w -ffast-math -funroll-loops
+#CPLUSPLUS = /export/soft/intel2015/impi/5.0.2.044/intel64/bin/mpiicpc
+#CXXFLAGS = -std=c++11 -O3 -openmp
+#CPLUSPLUS_GPROF = g++ -gp
+#CPLUSPLUS_MPI = /opt/openmpi/bin/mpicxx -O3 -w 
+#CPLUSPLUS_MPI=/export/soft/intel2015/impi/5.0.2.044/intel64/bin/mpiicpc
+
+### Einstein
+#CPLUSPLUS_MPI = /opt/openmpi-intel9/bin/mpicxx -O3 -w
+
+#LIBS=-L/export/soft/intel2015/composer_xe_2015.1.133/mkl/lib/intel64 -i-dynamic  -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -lpthread \
+
+### Version TC4600 wszhang
+CPLUSPLUS     = /opt/hpcx/2.9.0/ompi-icc/2019.update5/bin/mpicxx
+CPLUSPLUS_MPI = /opt/hpcx/2.9.0/ompi-icc/2019.update5/bin/mpicxx
+CXXFLAGS      = -std=c++11 -O2 -xCORE-AVX2 -align -fma -ftz -fomit-frame-pointer -finline-functions \
+                -I${MKLROOT}/include -I${MKLROOT}/include/intel64/ilp64
+LIBS          = -L${MKLROOT}/lib/intel64 \
+                -lmkl_blacs_intelmpi_lp64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core  -lpthread -limf  
+
+ 
+
+TOOLS_OBJS=src_tools/mathzone.o \
+			src_tools/matrix.o \
+			src_tools/matrix3.o \
+			src_tools/realarray.o \
+			src_tools/intarray.o \
+			src_tools/complexmatrix.o \
+			src_tools/complexarray.o\
+			src_tools/timer.o \
+			src_tools/inverse_matrix.o\
+			src_tools/inverse_matrix_iterate.o\
+			src_tools/Simulated_Annealing.o\
+
+SPILLAGE_OBJS=src_spillage/main.o \
+			  src_spillage/read_INPUT.o\
+			  src_spillage/ReadData.o\
+			  src_spillage/Calculate_C4.o\
+			  src_spillage/Coefficients.o\
+			  src_spillage/MultiZeta.o\
+			  src_spillage/SpillageStep.o\
+			  src_spillage/SpillageValue.o\
+			  src_spillage/Step_Data.o\
+			  src_spillage/Inverse_Matrix_S.o\
+			  src_spillage/Orthogonal.o\
+			  src_spillage/Type_Information.o\
+			  src_spillage/Metropolis.o\
+			  src_spillage/Metropolis_2.o\
+			  src_spillage/Out_Orbital.o\
+			  src_spillage/Plot_Psi.o\
+			  src_spillage/Psi_Second.o\
+			  src_spillage/tools.o \
+			  src_spillage/common.o \
+
+PARALLEL_OBJS=src_parallel/parallel_global.o\
+	src_parallel/parallel_common.o\
+	src_parallel/parallel_reduce.o\
+	src_parallel/parallel_kpoints.o	
+
+PW_OBJS=src_pw/pw_basis.o\
+	src_pw/pw_complement.o\
+	src_pw/heapsort.o\
+	src_pw/numerical_basis.o\
+	src_pw/bessel_basis.o\
+	src_pw/ylm_real.o\
+	src_pw/memory_calculation.o\
+			  
+OBJS = ${TOOLS_OBJS} \
+	   ${SPILLAGE_OBJS} \
+	   ${PARALLEL_OBJS} \
+	   ${PW_OBJS}\
+
+help : 
+	@echo 'make target list: '
+	@echo 's : Series version of Monte Carlo Spillage Program.'
+	@echo 'p : Parallel Version of Monte Carlo Spillage Program.'
+	@echo 'note : some notes.'
+
+s : ${OBJS} 
+	${CPLUSPLUS} ${CXXFLAGS} -o SIA_s.exe ${OBJS} ${LIBS}
+
+p : ${OBJS}
+	$(CPLUSPLUS_MPI) -D__MPI ${CXXFLAGS} -o SIA_p.exe $(OBJS) $(LIBS)
+
+note :
+	@echo 'atom type label           : it '
+	@echo 'atom label for each type  : ia '
+	@echo 'The angular momentum      : l '
+	@echo 'The multiplicity          : n '
+	@echo 'The magnetic quantum num  : m '
+	@echo 'The k point index         : ik '
+	@echo 'The band index            : ib '
+	@echo 'The eigenvalue of Jlq     : ie '
+	@echo 'The radius cutoff (a.u.)  : rcut '
+	@echo 'The state is              : psi(ib,ik) '
+	@echo 'The local orbitals is     : phi(it,ia,l,n,m) '
+	@echo 'The index of local basis  : nwfc(it,l,n)'
+	@echo 'The index of local basis  : nwfc2(it,ia,l,n,m) '
+	@echo 'The Spherical Bessel func : Jl(ie,rcut) '
+	@echo 'The SB transform          : \int Jl(ie,rcut) * Jl'
+	@echo 'The index of Jlq coef     : Coef(it,l,n,ie)'
+	@echo 'The local orbitals formu  : phi=\sum_{ie} Coef(it,l,n,ie) * Jl(ie,rcut)'
+	@echo 'The spillage formula is   : S = <psi|(1-P)|psi>'
+	@echo 'The projector P is        : P = \sum_{mu,nu} |phi_mu> S^{-1} <phi_nu| '
+	@echo 'The orthogonal formula is : |psi2> = (1-P1) |psi1>'
+	@echo 'So we can fonud that      : P1|psi2> = 0 '
+	@echo 'the Q matrix is           : Q = <Jlq|psi> '
+	@echo 'the S matrix is           : S = <Jlq|Jlq> '
+	@echo 'start index of band       : BANDS_START(count from 1, not 0) '
+	@echo 'end index of band         : BANDS_END '
+
+.cpp.o:
+	${CPLUSPLUS} ${CXXFLAGS} -c $< -o $@
+#	$(CPLUSPLUS_MPI) -c -D__MPI $< -o $@
+
+.PHONY:clean
+clean:
+	${RM} *.o *.exe core* src_tools/*.o src_spillage/*.o tests_s/ORBITAL* tests_s/ORBITAL* src_parallel/*.o src_pw/*.o