adding comments to inputs.json files description in docs; and possibi…

…lity to not generate nanoscale logs

README.md

@@ -58,7 +58,8 @@ ll /path/to/simulation
 ... lammps_scripts_ffname -> /path/to/SCEMa/lammps_scripts_opls
 ... macroscale_input
 ... nanoscale_input
-... clustering -> /path/to/SCEMa/clustering
+... clustering -> /path/to/SCEMa/clustering # when using clustering algorithm to determine and eliminate redundant molecular simulations
+... surrogate_model -> /path/to/SCEMa/surrogate_model # when using a surrogate for molecular simulations ("stress computation method: 2")
 ```
 
 Most, if not all, of the simulation parameters are found in the configuration file `inputs_testname.json`:
@@ -70,7 +71,7 @@ cat /path/to/simulation/inputs_testname.json
 		"strain rate": 0.002
  	},
   "scale-bridging":{
-    "activate md update": 1,
+    "stress computation method": 0,
     "approximate md with hookes law": 0,
     "use pjm scheduler": 0
   },
@@ -140,7 +141,7 @@ cat /path/to/simulation/inputs_testname.json
     "macroscale restart": "./macroscale_restart",
     "nanoscale restart": "./nanoscale_restart",
     "macroscale log": "./macroscale_log",
-    "nanoscale log": "./nanoscale_log"
+    "nanoscale log": "none"
   }
 }
 ```

dealammps.cc

@@ -184,8 +184,6 @@ namespace HMM
 		std::string			nanostatelocout;
 		std::string			nanostatelocres;
 		std::string			nanologloc;
-		std::string			nanologloctmp;
-		std::string			nanologlochom;
 
 		std::string			md_scripts_directory;
 
@@ -391,9 +389,9 @@ namespace HMM
 
 		mkdir(nanostatelocout.c_str(), ACCESSPERMS);
 		mkdir(nanostatelocres.c_str(), ACCESSPERMS);
-		mkdir(nanologloc.c_str(), ACCESSPERMS);
-		nanologloctmp = nanologloc+"/tmp"; mkdir(nanologloctmp.c_str(), ACCESSPERMS);
-		nanologlochom = nanologloc+"/homog"; mkdir(nanologlochom.c_str(), ACCESSPERMS);
+		if(nanologloc != "none"){
+			mkdir(nanologloc.c_str(), ACCESSPERMS);
+		}
 
 		char fnset[1024]; sprintf(fnset, "%s/in.set.lammps", md_scripts_directory.c_str());
 		char fnstrain[1024]; sprintf(fnstrain, "%s/in.strain.lammps", md_scripts_directory.c_str());
@@ -508,8 +506,7 @@ namespace HMM
 		hcout << " Initialization of the Multiple Molecular Dynamics problem...       " << std::endl;
 		if(mmd_pcolor==0) mmd_problem->init(start_timestep, md_timestep_length, md_temperature,
 											   md_nsteps_sample, md_strain_rate, md_force_field, nanostatelocin,
-											   nanostatelocout, nanostatelocres, nanologloc,
-											   nanologloctmp, nanologlochom, macrostatelocout,
+											   nanostatelocout, nanostatelocres, nanologloc, macrostatelocout,
 											   md_scripts_directory, freq_checkpoint, freq_output_homog,
 											   machine_ppn, mdtype, cg_dir, nrepl,
 											   use_pjm_scheduler, input_config, approx_md_with_hookes_law);

docs/configuration.md

@@ -7,25 +7,25 @@ mpirun /path/to/SCEMa/build/dealammps configuration.json
 The JSON configuration file must be shaped as follows:
 ```
 {
-	"problem type":{
-		"class": "testname",
-		"strain rate": 0.002
- 	},
+  "problem type":{
+    "class": "dogbone" or "compact" or "dropweight",
+    "strain rate": 0.002
+  },
   "scale-bridging":{
-    "activate md update": 1,
-    "approximate md with hookes law": 0,
+    "stress computation method": 0 (molecular model) or 1 (analytical hooke's law) or 2 (surrogate model),
+    "approximate md with hookes law": 0 (normal mode) or 1 (debug mode, replaces LAMMPS kernel with simple dot product operation),
     "use pjm scheduler": 0
   },
   "continuum time":{
     "timestep length": 5.0e-7,
     "start timestep": 1,
-    "end timestep": 10
+    "end timestep": 500
   },
   "continuum mesh":{
     "fe degree": 1,
     "quadrature formula": 2,
     "input": {
-      "style" : "cuboid",
+      "style" : "cuboid" (for dogbone or dropweight) or "file3D" (for dogbone or compact),
       "x length" : 0.03,
       "y length" : 0.03,
       "z length" : 0.08,
@@ -39,10 +39,10 @@ The JSON configuration file must be shaped as follows:
       "min quadrature strain norm": 1.0e-10
     },
     "clustering":{
-      "points": 10,
-      "min steps": 5,
-      "diff threshold": 0.000001,
-      "scripts directory": "./clustering"
+      "points": 10 (number of points in the spline approximation of the strain trajectory),
+      "min steps": 5 (number of steps before the clustering algorithm kicks in, if 5 then algorithm starts at timestep 6), 
+      "diff threshold": 0.000001 (when the L2-norm distance of 2 splines exceeds this threshold they are considered different), 
+      "scripts directory": "./clustering" (directory where the python scripts for the clustering algorithm are located)
     }
   },
   "molecular dynamics material":{
@@ -51,26 +51,27 @@ The JSON configuration file must be shaped as follows:
     "distribution": {
       "style": "uniform",
       "proportions": [1.0]
-	  },
+    },
     "rotation common ground vector":[1.0, 0.0, 0.0]
   },
   "molecular dynamics parameters":{
     "temperature": 300.0,
     "timestep length": 2.0,
     "strain rate": 1.0e-4,
     "number of sampling steps": 100,
-    "scripts directory": "./lammps_scripts_ffname",
-    "force field": "ffname"
+    "scripts directory": "./lammps_scripts_opls" or "./lammps_scripts_reax",
+    "force field": "opls" or "reax"
   },
   "computational resources":{
     "machine cores per node": 24,
-    "number of nodes for FEM simulation": 1,
-    "minimum nodes per MD simulation": 1
+    "maximum number of cores for FEM simulation": 10,
+    "minimum number of cores for MD simulation": 1
   },
   "output data":{
-    "checkpoint frequency": 1,
+    "checkpoint frequency": 100,
     "visualisation output frequency": 1,
     "analytics output frequency": 1,
+  "loaded boundary force output frequency": 1,
     "homogenization output frequency": 1000
   },
   "directory structure":{
@@ -81,9 +82,9 @@ The JSON configuration file must be shaped as follows:
     "macroscale restart": "./macroscale_restart",
     "nanoscale restart": "./nanoscale_restart",
     "macroscale log": "./macroscale_log",
-    "nanoscale log": "./nanoscale_log"
+    "nanoscale log": "./nanoscale_log" or "none" (if no nanoscale log)
   }
 }
 
-## Description
+```
 

headers/md_sim.h

@@ -20,7 +20,7 @@ namespace HMM {
 			}
 
 			int qp_id;
-      int most_recent_qp_id;
+			int most_recent_qp_id;
 			int replica;
 			int material;
 			std::string matid;
@@ -47,10 +47,11 @@ namespace HMM {
 			bool output_homog; // what is this? seems to add an extra dump of atom coords	
 			bool checkpoint;
 
-			void define_file_names(std::string nanologloctmp)
+			void define_file_names(std::string nanologloc)
 			{
-    	  			log_file = nanologloctmp + "/" + time_id  + "." + std::to_string(qp_id) + "." + matid + "_" + std::to_string(replica);
-				// Preparing directory to write MD simulation log files
+    	  		if(nanologloc != "none") log_file = nanologloc + "/" + time_id  + "." + std::to_string(qp_id) + "." + matid + "_" + std::to_string(replica);
+    	  		else log_file = "none";
+    	  		// Preparing directory to write MD simulation log files
 				//mkdir(log_file.c_str(), ACCESSPERMS);
 			}		
 		private:

headers/stmd_problem.h

@@ -82,7 +82,11 @@ STMDProblem<dim>::~STMDProblem ()
 template <int dim>
 SymmetricTensor<2,dim> STMDProblem<dim>::lammps_straining (MDSim<dim> md_sim)
 {
-	mkdir(md_sim.log_file.c_str(), ACCESSPERMS);
+	bool store_log = true;
+	if (md_sim.log_file == "none") store_log = false;
+
+	if(store_log) mkdir(md_sim.log_file.c_str(), ACCESSPERMS);
+
 	char locff[1024]; /*reaxff*/
 	if (md_sim.force_field == "reax"){
 		sprintf(locff, "%s/ffield.reax.2", md_sim.scripts_folder.c_str()); /*reaxff*/
@@ -95,8 +99,10 @@ SymmetricTensor<2,dim> STMDProblem<dim>::lammps_straining (MDSim<dim> md_sim)
 	sprintf(initdata, "%s/init.%s.bin", md_sim.output_folder.c_str(), mdstate);
 
 	char homogdata_time[1024];
-	sprintf(homogdata_time, "%s/%s.%d.%s.lammpstrj", md_sim.log_file.c_str(),
-			md_sim.time_id.c_str(), md_sim.qp_id, mdstate);
+	if(store_log) {
+		sprintf(homogdata_time, "%s/%s.%d.%s.lammpstrj", md_sim.log_file.c_str(),
+				md_sim.time_id.c_str(), md_sim.qp_id, mdstate);
+	}
 
 	char straindata_lcts[1024];
 	sprintf(straindata_lcts, "%s/lcts.%d.%s.dump", md_sim.restart_folder.c_str(),
@@ -141,15 +147,16 @@ SymmetricTensor<2,dim> STMDProblem<dim>::lammps_straining (MDSim<dim> md_sim)
 	lmparg[2] = (char *) "none";
 	lmparg[3] = (char *) "-log";
 	lmparg[4] = new char[1024];
-	sprintf(lmparg[4], "%s/log.stress_strain", md_sim.log_file.c_str());
+	if(store_log) sprintf(lmparg[4], "%s/log.stress_strain", md_sim.log_file.c_str());
+	else sprintf(lmparg[4], "none");
 
 	// Creating LAMMPS instance
 	LAMMPS *lmp = NULL;
 	lmp = new LAMMPS(nargs,lmparg,md_batch_communicator);
 
 	// Passing location for output as variable
 	sprintf(cline, "variable mdt string %s", md_sim.matid.c_str()); lammps_command(lmp,cline);
-	sprintf(cline, "variable loco string %s", md_sim.log_file.c_str()); lammps_command(lmp,cline);
+	if(store_log) {sprintf(cline, "variable loco string %s", md_sim.log_file.c_str()); lammps_command(lmp,cline);}
 	sprintf(cline, "variable locs string %s", md_sim.scripts_folder.c_str()); lammps_command(lmp,cline);
 
 	// Setting testing temperature
@@ -271,10 +278,11 @@ SymmetricTensor<2,dim> STMDProblem<dim>::lammps_straining (MDSim<dim> md_sim)
 				<< "Homogenization of stiffness and stress using in.elastic.lammps...       " << std::endl;*/
 
 	// Creating LAMMPS instance
-	sprintf(lmparg[4], "%s/log.homogenization", md_sim.log_file.c_str());
+	if(store_log) sprintf(lmparg[4], "%s/log.homogenization", md_sim.log_file.c_str());
+	else sprintf(lmparg[4], "none");
 	lmp = new LAMMPS(nargs,lmparg,md_batch_communicator);
 
-	sprintf(cline, "variable loco string %s", md_sim.log_file.c_str()); lammps_command(lmp,cline);
+	if(store_log) {sprintf(cline, "variable loco string %s", md_sim.log_file.c_str()); lammps_command(lmp,cline);}
 	sprintf(cline, "variable locs string %s", md_sim.scripts_folder.c_str()); lammps_command(lmp,cline);
 
 	// Setting testing temperature
@@ -301,7 +309,7 @@ SymmetricTensor<2,dim> STMDProblem<dim>::lammps_straining (MDSim<dim> md_sim)
 
 	sprintf(cline, "variable dts equal %f", md_sim.timestep_length); lammps_command(lmp,cline);
 
-	if(md_sim.output_homog){
+	if(md_sim.output_homog && store_log){
 		// Setting dumping of atom positions for post analysis of the MD simulation
 		// DO NOT USE CUSTOM DUMP: WRONG ATOM POSITIONS...
 		sprintf(cline, "dump atom_dump all atom %d %s", 1, homogdata_time); lammps_command(lmp,cline);
@@ -399,15 +407,17 @@ SymmetricTensor<2,dim> STMDProblem<dim>::lammps_straining (MDSim<dim> md_sim)
 	// close down LAMMPS
 	delete lmp;
 
-	// Clean "nanoscale_logs" of the finished timestep
-	char command[1024];
-	sprintf(command, "rm -rf %s", md_sim.log_file.c_str());
-	//std::cout<< "Logfile "<< md_simulation.log_file <<std::endl;
-	int ret = system(command);
-	if (ret!=0){
-		std::cout << "Failed removing the log files of the MD simulation: " << md_sim.log_file << std::endl;
+	if(store_log) {
+		// Clean "nanoscale_logs" of the finished timestep
+		char command[1024];
+		sprintf(command, "rm -rf %s", md_sim.log_file.c_str());
+		//std::cout<< "Logfile "<< md_simulation.log_file <<std::endl;
+		int ret = system(command);
+		if (ret!=0){
+			std::cout << "Failed removing the log files of the MD simulation: " << md_sim.log_file << std::endl;
+		}
+		//boost::filesystem::remove_all(md_sim.log_file.c_str());
 	}
-	//boost::filesystem::remove_all(md_sim.log_file.c_str());
 	return md_sim.stress;
 }
 

headers/stmd_sync.h

@@ -62,7 +62,7 @@ class STMDSync
 	~STMDSync ();
 	void init (int sstp, double mdtlength, double mdtemp, int nss, double strr, std::string ffi,
 			std::string nslocin, std::string nslocout, std::string nslocres, std::string nlogloc,
-			std::string nlogloctmp,std::string nloglochom, std::string mslocout, std::string mdsdir,
+			std::string mslocout, std::string mdsdir,
 			int fchpt, int fohom, unsigned int mppn,
 			std::vector<std::string> mdt, Tensor<1,dim> cgd, unsigned int nr, bool ups,
 			boost::property_tree::ptree inconfig, bool approx_md_with_hookes_law);
@@ -147,8 +147,6 @@ class STMDSync
 	std::string							nanostatelocout;
 	std::string							nanostatelocres;
 	std::string							nanologloc;
-	std::string							nanologloctmp;
-	std::string							nanologlochom;
 
 	std::string							md_scripts_directory;
 	bool								use_pjm_scheduler;
@@ -368,7 +366,7 @@ void STMDSync<dim>::load_replica_equilibration_data ()
 			stressoutputfile[imdrun] = nanostatelocin + "/init." + mdtype[imdt] + "_" + std::to_string(numrepl) + ".stress";
 			stiffoutputfile[imdrun] = nanostatelocin + "/init." + mdtype[imdt] + "_" + std::to_string(numrepl) + ".stiff";
 			systemoutputfile[imdrun] = nanostatelocin + "/init." + mdtype[imdt] + "_" + std::to_string(numrepl) + ".bin";
-			qpreplogloc[imdrun] = nanologloctmp + "/init" + "." + mdtype[imdt] + "_" + std::to_string(numrepl);
+			qpreplogloc[imdrun] = nanologloc + "/init" + "." + mdtype[imdt] + "_" + std::to_string(numrepl);
 		}
 	}
 
@@ -523,7 +521,7 @@ std::vector< MDSim<dim> > STMDSync<dim>::prepare_md_simulations(ScaleBridgingDat
 			md_sim.checkpoint 			= checkpoint_save;
 			// Setting up location for temporary log outputs of md simulation, input strains and output stresses
 			std::string macrostatelocout = input_config.get<std::string>("directory structure.macroscale output");
-			if (approx_md_with_hookes_law == false) md_sim.define_file_names(nanologloctmp);
+			if (approx_md_with_hookes_law == false) md_sim.define_file_names(nanologloc);
 
 			// Argument of the MD simulation: strain to apply
 			SymmetricTensor<2,dim> cg_loc_rep_strain(scale_bridging_data.update_list[qp].update_strain);
@@ -745,7 +743,7 @@ void STMDSync<dim>::generate_job_list(bool& elmj, int& tta, char* filenamelist)
 
 	sprintf(command, "python ../optimization_pjm/optimization_hmm.py %s %d %d %s %s %s %s",
 			macrostatelocout.c_str(), 1, nrepl, time_id.c_str(),
-			nanostatelocout.c_str(), nanologloctmp.c_str(), filenamelist);
+			nanostatelocout.c_str(), nanologloc.c_str(), filenamelist);
 
 	// Executing the job list optimization script with fscanf to parse the printed values from the python script
 	FILE* in = popen(command, "r");
@@ -918,8 +916,7 @@ void STMDSync<dim>::store_md_simulations(std::vector<MDSim<dim> > md_simulations
 
 template <int dim>
 void STMDSync<dim>::init (int sstp, double mdtlength, double mdtemp, int nss, double strr, std::string ffi,
-		std::string nslocin, std::string nslocout, std::string nslocres, std::string nlogloc,
-		std::string nlogloctmp,std::string nloglochom, std::string mslocout,
+		std::string nslocin, std::string nslocout, std::string nslocres, std::string nlogloc, std::string mslocout,
 		std::string mdsdir, int fchpt, int fohom, unsigned int mppn,
 		std::vector<std::string> mdt, Tensor<1,dim> cgd, unsigned int nr, bool ups,
 		boost::property_tree::ptree inconfig, bool hookeslaw){
@@ -939,8 +936,6 @@ void STMDSync<dim>::init (int sstp, double mdtlength, double mdtemp, int nss, do
 	nanostatelocout = nslocout;
 	nanostatelocres = nslocres;
 	nanologloc = nlogloc;
-	nanologloctmp = nlogloctmp;
-	nanologlochom = nloglochom;
 
 	macrostatelocout = mslocout;
 	md_scripts_directory = mdsdir;

init_material.cc

@@ -101,7 +101,6 @@ namespace HMM
 		std::string                         nanostatelocin;
 		std::string							nanostatelocout;
 		std::string							nanologloc;
-		std::string							nanologloctmp;
 
 		std::string							md_scripts_directory;
 
@@ -238,8 +237,9 @@ namespace HMM
 			exit(1);
 		}
 
-		mkdir(nanologloc.c_str(), ACCESSPERMS);
-		nanologloctmp = nanologloc+"/tmp"; mkdir(nanologloctmp.c_str(), ACCESSPERMS);
+		if(nanologloc != "none"){
+			mkdir(nanologloc.c_str(), ACCESSPERMS);
+		}
 
 		char fnset[1024]; sprintf(fnset, "%s/in.set.lammps", md_scripts_directory.c_str());
 		char fnstrain[1024]; sprintf(fnstrain, "%s/in.strain.lammps", md_scripts_directory.c_str());

input_configurations/inputs_dogbone_file3D.json

@@ -46,8 +46,8 @@
     "timestep length": 2.0,
     "strain rate": 2.0e-4,
     "number of sampling steps": 100,
-    "scripts directory": "./lammps_scripts_opls",
-    "force field": "opls"
+    "scripts directory": "./lammps_scripts_reax",
+    "force field": "reax"
   },
   "computational resources":{
     "machine cores per node": 24,
@@ -69,6 +69,6 @@
     "macroscale restart": "./macroscale_restart",
     "nanoscale restart": "./nanoscale_restart",
     "macroscale log": "./macroscale_log",
-    "nanoscale log": "./nanoscale_log"
+    "nanoscale log": "none"
   }
 }