Added NOMAD2XYZ app (used for preprocessing json into remote visualization

ready datasets).

NOMADVRLib/ConfigFile.cpp

@@ -36,9 +36,6 @@ float scaling;
 float markerscaling;
 
 float BACKGROUND[3];
-int* numAtoms; //[timesteps]
-float **atoms; //[timesteps][numAtoms[i]*4] //xyzu, u=atom number
-bool fixedAtoms; 
 
 float atomScaling;
 std::vector<float> *clonedAtoms;
@@ -55,11 +52,8 @@ bool showTrajectories;
 std::vector<int> atomtrajectories;
 std::vector<std::vector<int>> atomtrajectoryrestarts;
 
-float abc[3][3]; //basis vectors
-bool has_abc = false;
 bool displayunitcell;
-float supercell[3];
-int voxelSize[3];
+
 float unitcellcolour[4];
 float supercellcolour[4];
 
@@ -79,7 +73,6 @@ float nearclip, farclip;
 //markers such as hole positions and electron positions
 float ** markers;
 float ** markercolours;
-float cubetrans[3];
 
 float animationspeed;
 float movementspeed;

NOMADVRLib/ConfigFile.h

@@ -19,6 +19,7 @@
 #include <vector>
 #include "MyGL.h"
 #include "polyhedron.h"
+#include "ConfigFileAtoms.h"
 
 extern const char * PATH;
 extern const char * SCREENSHOT;
@@ -31,9 +32,7 @@ extern float userpos[3];
 extern float scaling;
 
 extern float BACKGROUND[3];
-extern int* numAtoms; //[timesteps]
-extern float **atoms; //[timesteps][numAtoms[i]*4] //xyzu, u=atom number
-extern bool fixedAtoms; //all timesteps use the atoms for timestep 0. Used for excitons etc.
+
 extern float atomScaling;
 extern std::vector<float> *clonedAtoms;
 extern std::vector<int> bonds;
@@ -49,10 +48,8 @@ extern bool showTrajectories;
 extern std::vector<int> atomtrajectories;
 extern std::vector<std::vector<int>> atomtrajectoryrestarts;
 
-extern float abc[3][3]; //basis vectors
-extern bool has_abc;
 extern bool displayunitcell;
-extern float supercell[3];
+
 extern float markerscaling;
 extern float unitcellcolour[4];
 extern float supercellcolour[4];
@@ -79,8 +76,6 @@ extern float movementspeed;  //how fast to move the user
 //markers such as hole positions and electron positions
 extern float ** markers;
 extern float ** markercolours;
-extern float cubetrans[3];
-extern int voxelSize[3];
 
 extern const char * loadConfigFileErrors[];
 

NOMADVRLib/ConfigFileAtoms.cpp

+float abc[3][3]; //basis vectors
+bool has_abc = false;
+
+int* numAtoms; //[timesteps]
+float **atoms; //[timesteps][numAtoms[i]*4] //xyzu, u=atom number
+bool fixedAtoms; 
+
+float cubetrans[3];
+
+float supercell[3];
+int voxelSize[3];
\ No newline at end of file

NOMADVRLib/ConfigFileAtoms.h

+#ifndef CONFIGFILEATOMS_H
+#define CONFIGFILEATOMS_H
+
+extern float abc[3][3]; //basis vectors
+extern bool has_abc;
+
+extern int* numAtoms; //[timesteps]
+extern float **atoms; //[timesteps][numAtoms[i]*4] //xyzu, u=atom number
+extern bool fixedAtoms; //all timesteps use the atoms for timestep 0. Used for excitons etc.
+
+extern float cubetrans[3];
+extern int voxelSize[3];
+
+extern float supercell[3];
+
+#endif //CONFIGFILEATOMS_H

NOMADVRLib/atoms.cpp

@@ -28,7 +28,7 @@
 
 #include "eprintf.h"
 #include "atoms.hpp"
-#include "ConfigFile.h"
+#include "ConfigFileAtoms.h"
 #include "rapidjson/document.h" 
 #include "rapidjson/filereadstream.h"
 #include "happyhttp/happyhttp.h"

NOMADVRLib/atoms.hpp

@@ -62,6 +62,7 @@ void TransformAtoms(std::vector<float>* clonedAtoms, const float abc[3][3]);
 extern bool inv_abc_init;
 extern float inv_abc[3][3];
 
+extern const char * const atomNames[];
 extern std::vector<const char*> extraAtomNames;
 extern std::vector<float*> extraAtomData;
 

README.md

@@ -3,6 +3,9 @@ Subdirectories:
 	OculusMobile: Demos for GearVR.
 	GoogleCardboardAndroid: Demos for Google Cardboard (android)
 	CAVE: Demos for LRZ CAVE-like environment (linux)
+
+	NOMADGearVRChooser: Android app to select the dataset for GearVR, which
+		calls the OculusMobile app as a subroutine.
 	
 	NOMADVRLib: Shared code between HTC Vive, GearVR and Google Cardboard demos related to NOMAD.
 	libs: Other (external) supporting libs shared by HTC Vive, GearVR, Cardboard and CAVE demos
@@ -11,6 +14,10 @@ Subdirectories:
 		htdocs: Web pages containing the VR software and documentation.
 		cgi-bin: cgi scripts to create suitable config files from a material number.
 	
+	RemoteVisualization: NOMAD2xyz app 
+		Transforms a json from encyclopedia or archive into an XYZ file	
+		Useful for the remote visualization infrastructure
+	
 More platforms will be added in the future.
 
 The code is distributed under the Apache 2.0 License (See LICENSE file).

RemoteVisualization/Makefile

+all: NOMADVRLib/atoms.o eprintf.o happyhttp/happyhttp.o NOMADVRLib/ConfigFileAtoms.o main.o
+	g++ $^ -o nomad2xyz
+
+.cpp.o:
+	g++ -I. -std=c++11 $< -c -o $*.o
+
+clean:
+	rm -f *.o nomad2xyz

RemoteVisualization/Readme.txt

+NOMAD2xyz app 
+	Transforms a json from encyclopedia or archive into an XYZ file	
+	Useful for the remote visualization infrastructure
+
+Depends on the following libraries:
+	NOMADVRLib
+	happyhttp
+	rapidjson
\ No newline at end of file

RemoteVisualization/eprintf.cpp

+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+*/
+
+#include <stdarg.h>
+#include <stdio.h>
+
+#include "NOMADVRLib/eprintf.h"
+
+void eprintf( const char *fmt, ... )
+{
+	va_list args;
+	char buffer[ 2048 ];
+
+	va_start( args, fmt );
+	vsprintf( buffer, fmt, args );
+	va_end( args );
+
+	fprintf(stderr, "%s\n", buffer );
+}

RemoteVisualization/main.cpp

+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+*/
+
+#include "NOMADVRLib/eprintf.h"
+#include "NOMADVRLib/ConfigFileAtoms.h"
+#include "NOMADVRLib/atoms.hpp"
+
+	int timesteps;
+
+void exportXYZ(const char * file, const char *mat)
+{
+
+FILE * f=fopen (file, "w");
+for (int i=0;i<timesteps;i++) {
+	fprintf (f, "%d\n", numAtoms[i]);
+	fprintf (f, "Comment: Material=%s\n", mat);
+
+	for (int j=0;j<numAtoms[i];j++) {
+		fprintf (f, "%s\t%f\t%f\t%f\n", atomNames[(int)(atoms[i][j*4+3])], 
+			atoms[i][j*4+0], atoms[i][j*4+1], atoms[i][j*4+2]);
+
+
+	}
+}
+}
+
+void usage (const char * argv0) 
+{
+        eprintf ("Usage: \n%s e <basename for encyclopedia json> xyz", argv0);
+        eprintf ("%s a <archive json> xyz", argv0);
+
+}
+
+int main (int argc, char **argv) {
+
+	if (argc < 3) {
+		usage(argv[0]);
+		return 1;
+	}
+
+	std::vector<float> *clonedAtoms;
+	if (argv[1][0]=='e') {
+		readAtomsJson (argv[2], &numAtoms, &timesteps, &atoms, abc, &clonedAtoms);
+	
+		//now export xyz
+		exportXYZ(argv[3], argv[2]);
+	} else if (argv[1][0]=='a') {
+		readAtomsAnalyticsJson (argv[2], &numAtoms, &timesteps, &atoms, abc, &clonedAtoms);
+		exportXYZ (argv[3], argv[2]);
+	} else {
+		usage(argv[0]);	
+		return 2;
+	}
+	return 0;
+}