Merge pull request #22 from UCL-CCS/surrogate

Surrogate

CMakeLists/myriad.CMakeLists.txt

@@ -1,7 +1,7 @@
 CMAKE_MINIMUM_REQUIRED(VERSION 2.8.8)
 
 FIND_PACKAGE(deal.II 8.4.1 QUIET
-  HINTS ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
+  HINTS /home/uccamva/opt/dealii-9.0.0/ ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
   )
 IF(NOT ${deal.II_FOUND})
   MESSAGE(FATAL_ERROR "\n"
@@ -26,17 +26,19 @@ DEAL_II_SETUP_TARGET(strain_md)
 
 ## Include LAMMPS sources repository
 INCLUDE_DIRECTORIES(
-  /shared/ucl/apps/lammps/16Mar18/USERINTEL/intel-2018/lammps-16Mar18/src/
+  /home/uccamva/sources/lammps-17Nov16/src/
+  /home/uccamva/.conda/envs/surrogate/include/python3.8/
   )
 
 ## Include BOOST sources repository
 #FIND_PACKAGE( Boost 1.58 COMPONENTS filesystem mpi REQUIRED )
 #INCLUDE_DIRECTORIES( ${Boost_INCLUDE_DIR} )
 
 ## Include LAMMPS library shared .so (or static .a)
-TARGET_LINK_LIBRARIES(dealammps ~/.local/lib64/liblammps.so)
-TARGET_LINK_LIBRARIES(init_material ~/.local/lib64/liblammps.so)
-TARGET_LINK_LIBRARIES(strain_md ~/.local/lib64/liblammps.so)
+TARGET_LINK_LIBRARIES(dealammps /home/uccamva/sources/lammps-17Nov16/src/liblammps.so)
+TARGET_LINK_LIBRARIES(dealammps /home/uccamva/.conda/envs/surrogate/lib/libpython3.8.so)
+TARGET_LINK_LIBRARIES(init_material /home/uccamva/sources/lammps-17Nov16/src/liblammps.so)
+TARGET_LINK_LIBRARIES(strain_md /home/uccamva/sources/lammps-17Nov16/src/liblammps.so)
 
 TARGET_LINK_LIBRARIES(dealammps LINK_PUBLIC ${Boost_LIBRARIES})
 TARGET_LINK_LIBRARIES(init_material LINK_PUBLIC ${Boost_LIBRARIES})

dealammps.cc

@@ -159,7 +159,7 @@ namespace HMM
 		Tensor<1,dim> 			cg_dir;
 		boost::property_tree::ptree	input_config;
 
-		bool				activate_md_update;
+		int					stress_compute_method;
 		bool				approx_md_with_hookes_law;
 		bool				use_pjm_scheduler;
 
@@ -236,7 +236,7 @@ namespace HMM
 	    quadrature_formula 	= input_config.get<int>("continuum mesh.quadrature formula");
 
 	    // Scale-bridging parameters
-	    activate_md_update 	= input_config.get<bool>("scale-bridging.activate md update");
+	    stress_compute_method 	= input_config.get<int>("scale-bridging.stress computation method");
 	    approx_md_with_hookes_law	=input_config.get<bool>("scale-bridging.approximate md with hookes law");
 	    use_pjm_scheduler 	= input_config.get<bool>("scale-bridging.use pjm scheduler");
 
@@ -294,7 +294,7 @@ namespace HMM
 
 		// Print a recap of all the parameters...
 		hcout << "Parameters listing:" << std::endl;
-		hcout << " - Activate MD updates (1 is true, 0 is false): "<< activate_md_update << std::endl;
+		hcout << " - Method to compute local stresses (0 - LAMMPS, 1 - Hooke's law, 2 - ML surrogate model): "<< stress_compute_method << std::endl;
 		hcout << " - Approximate MD sims with hookes law (1 is true, 0 is false): "<< approx_md_with_hookes_law << std::endl;
 		hcout << " - Use Pilot Job Manager to schedule MD jobs: "<< use_pjm_scheduler << std::endl;
 		hcout << " - FE timestep duration: "<< fe_timestep_length << std::endl;
@@ -523,7 +523,7 @@ namespace HMM
 										macrostatelocin, macrostatelocout,
 										macrostatelocres, macrologloc,
 										freq_checkpoint, freq_output_visu, freq_output_lhist, freq_output_lbcforce,
-										activate_md_update, mdtype, cg_dir,
+										stress_compute_method, mdtype, cg_dir,
 										twod_mesh_file, extrude_length, extrude_points, 
 										input_config, approx_md_with_hookes_law);
 

examples/streched_polyhedron/inputs.json

@@ -4,7 +4,7 @@
 		"strain rate": 0.002
  	},
   "scale-bridging":{
-    "activate md update": 1,
+    "stress computation method": 0,
     "approximate md with hookes law": 0,
     "use pjm scheduler": 0
   },
@@ -30,7 +30,7 @@
     "md":{
       "min quadrature strain norm": 1.0e-10
     },
-    "clustering":{
+  "clustering":{
       "spline points": 10,
       "min steps": 5000,
       "diff threshold": 0.000001,
@@ -56,14 +56,14 @@
   },
   "computational resources":{
     "machine cores per node": 24,
-    "maximum number of cores for FEM simulation": 1,
+		"maximum number of cores for FEM simulation": 1,
     "minimum number of cores for MD simulation": 1
   },
   "output data":{
     "checkpoint frequency": 1,
     "visualisation output frequency": 1,
     "analytics output frequency": 1,
-    "loaded boundary force output frequency": 1,
+		"loaded boundary force output frequency": 1,
     "homogenization output frequency": 1000
   },
   "directory structure":{

headers/FE.h

@@ -96,7 +96,7 @@ namespace HMM
 		SymmetricTensor<2,dim> upd_strain;
 		SymmetricTensor<2,dim> newton_strain;
 		MatHistPredict::Strain6D hist_strain;
-		bool to_be_updated;
+		bool to_be_updated_with_md;
 
 		// Characteristics
 		unsigned int qpid;
@@ -233,7 +233,7 @@ namespace HMM
 
 							void init (int sstp, double tlength, std::string mslocin, std::string mslocout,
 											std::string mslocres, std::string mlogloc, int fchpt, int fovis, int folhis, int folbcf,
-											bool actmdup, std::vector<std::string> mdt, Tensor<1,dim> cgd, 
+											int stress_method, std::vector<std::string> mdt, Tensor<1,dim> cgd,
 											std::string twodmfile, double extrudel, int extrudep, 
 											boost::property_tree::ptree inconfig, bool hookeslaw);
 							void beginstep (int tstp, double ptime);
@@ -272,6 +272,9 @@ namespace HMM
 							void gather_qp_update_list(ScaleBridgingData &scale_bridging_data);
 							template <typename T>
 							std::vector<T> gather_vector(std::vector<T> local_vector);
+							SymmetricTensor<2,dim> compute_stress_with_surrogate(SymmetricTensor<2,dim> old_strain,
+																				 SymmetricTensor<2,dim> new_strain,
+																				 SymmetricTensor<2,dim> old_stress);
 							void update_stress_quadrature_point_history
 									(const Vector<double>& displacement_update, ScaleBridgingData scale_bridging_data);
 							void clean_transfer();
@@ -360,7 +363,7 @@ namespace HMM
 							int									freq_output_lhist;
 							int									freq_output_lbcforce;
 
-							bool 								activate_md_update;
+							int 								stress_compute_method;
 
 							std::string		twod_mesh_file;
 							double                  extrude_length;