Multiuser OpenVR NOMAD VR functionality: show remote user position and

orientation of head and controllers.
Enable atom drag-and-drop functionality (with external helper).

NOMADVRLib/ConfigFile.cpp

@@ -213,6 +213,9 @@ void cleanConfig()
 		numAtoms=nullptr;
 		atoms=nullptr;
 	}
+
+	delete[] server;
+	server=nullptr;
 }
 
 void initState()

RemoteVisualization/Makefile

-all: NOMADVRLib/atoms.o eprintf.o happyhttp/happyhttp.o NOMADVRLib/ConfigFileAtoms.o main.o
+all: NOMADVRLib/atoms.o eprintf.o happyhttp/happyhttp.o NOMADVRLib/ConfigFileAtoms.o main.o exportXYZ.o 
 	g++ $^ -o nomad2xyz
 
 .cpp.o:

RemoteVisualization/exportXYZ.cpp

+#include <stdio.h>
+
+#include "NOMADVRLib/ConfigFileAtoms.h"
+#include "NOMADVRLib/atoms.hpp"
+#include "exportXYZ.h"
+
+void exportXYZ(const char * file, const char *mat, int timesteps)
+{
+
+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]);
+
+
+	}
+}
+}

RemoteVisualization/exportXYZ.h

+#ifndef __EXPORTXYZ_H
+#define __EXPORTXYZ_H
+
+void exportXYZ(const char * file, const char *mat, int timesteps);
+
+#endif

RemoteVisualization/main.cpp

@@ -17,26 +17,10 @@
 #include "NOMADVRLib/eprintf.h"
 #include "NOMADVRLib/ConfigFileAtoms.h"
 #include "NOMADVRLib/atoms.hpp"
+#include "exportXYZ.h"
 
 	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);
@@ -56,10 +40,10 @@ int main (int argc, char **argv) {
 		readAtomsJson (argv[2], &numAtoms, &timesteps, &atoms, abc, &clonedAtoms);
 	
 		//now export xyz
-		exportXYZ(argv[3], argv[2]);
+		exportXYZ(argv[3], argv[2], timesteps);
 	} else if (argv[1][0]=='a') {
 		readAtomsAnalyticsJson (argv[2], &numAtoms, &timesteps, &atoms, abc, &clonedAtoms);
-		exportXYZ (argv[3], argv[2]);
+		exportXYZ (argv[3], argv[2], timesteps);
 	} else {
 		usage(argv[0]);	
 		return 2;

proxy/MD-driver/Makefile

+all: PeriodicTable SimpleMove
+
+SimpleMove: SimpleMove.o PeriodicTable.o exportXYZ.o NOMADVRLib/ConfigFileAtoms.o NOMADVRLib/atoms.o \
+	happyhttp/happyhttp.o eprintf.o myrecv.o
+	g++ -g $^ -o $@
+
+PeriodicTable: PeriodicTable.o NOMADVRLib/ConfigFileAtoms.o NOMADVRLib/atoms.o exportXYZ.o happyhttp/happyhttp.o \
+	eprintf.o PeriodicTableMain.o
+	g++ -g $^ -o $@
+
+.cpp.o:
+	g++ -g -I. -std=c++11 $< -c -o $*.o
+
+clean:
+	rm -f *.o PeriodicTable SimpleMove
+

proxy/MD-driver/PT.xyz

+118
+Comment: Material=PeriodicTable
+H	0.000000	0.000000	0.000000
+He	17.000000	0.000000	0.000000
+Li	0.000000	0.000000	1.000000
+Be	1.000000	0.000000	1.000000
+B	10.000000	0.000000	1.000000
+C	11.000000	0.000000	1.000000
+N	12.000000	0.000000	1.000000
+O	13.000000	0.000000	1.000000
+F	14.000000	0.000000	1.000000
+Ne	15.000000	0.000000	1.000000
+Na	0.000000	0.000000	2.000000
+Mg	1.000000	0.000000	2.000000
+Al	10.000000	0.000000	2.000000
+Si	11.000000	0.000000	2.000000
+P	12.000000	0.000000	2.000000
+S	13.000000	0.000000	2.000000
+Cl	14.000000	0.000000	2.000000
+Ar	15.000000	0.000000	2.000000
+K	0.000000	0.000000	3.000000
+Ca	1.000000	0.000000	3.000000
+Sc	2.000000	0.000000	3.000000
+Ti	3.000000	0.000000	3.000000
+V	4.000000	0.000000	3.000000
+Cr	5.000000	0.000000	3.000000
+Mn	6.000000	0.000000	3.000000
+Fe	7.000000	0.000000	3.000000
+Co	8.000000	0.000000	3.000000
+Ni	9.000000	0.000000	3.000000
+Cu	10.000000	0.000000	3.000000
+Zn	11.000000	0.000000	3.000000
+Ga	12.000000	0.000000	3.000000
+Ge	13.000000	0.000000	3.000000
+As	14.000000	0.000000	3.000000
+Se	15.000000	0.000000	3.000000
+Br	16.000000	0.000000	3.000000
+Kr	17.000000	0.000000	3.000000
+Rb	0.000000	0.000000	4.000000
+Sr	1.000000	0.000000	4.000000
+Y	2.000000	0.000000	4.000000
+Zr	3.000000	0.000000	4.000000
+Nb	4.000000	0.000000	4.000000
+Mo	5.000000	0.000000	4.000000
+Tc	6.000000	0.000000	4.000000
+Ru	7.000000	0.000000	4.000000
+Rh	8.000000	0.000000	4.000000
+Pd	9.000000	0.000000	4.000000
+Ag	10.000000	0.000000	4.000000
+Cd	11.000000	0.000000	4.000000
+In	12.000000	0.000000	4.000000
+Sn	13.000000	0.000000	4.000000
+Sb	14.000000	0.000000	4.000000
+Te	15.000000	0.000000	4.000000
+I	16.000000	0.000000	4.000000
+Xe	17.000000	0.000000	4.000000
+Cs	0.000000	0.000000	5.000000
+Ba	1.000000	0.000000	5.000000
+La	2.000000	0.000000	5.000000
+Ce	4.000000	0.000000	9.000000
+Pr	5.000000	0.000000	9.000000
+Nd	6.000000	0.000000	9.000000
+Pm	7.000000	0.000000	9.000000
+Sm	8.000000	0.000000	9.000000
+Eu	9.000000	0.000000	9.000000
+Gd	10.000000	0.000000	9.000000
+Tb	11.000000	0.000000	9.000000
+Dy	12.000000	0.000000	9.000000
+Ho	13.000000	0.000000	9.000000
+Er	14.000000	0.000000	9.000000
+Tm	15.000000	0.000000	9.000000
+Yb	16.000000	0.000000	9.000000
+Lu	17.000000	0.000000	9.000000
+Hf	3.000000	0.000000	5.000000
+Ta	4.000000	0.000000	5.000000
+W	5.000000	0.000000	5.000000
+Re	6.000000	0.000000	5.000000
+Os	7.000000	0.000000	5.000000
+Ir	8.000000	0.000000	5.000000
+Pt	9.000000	0.000000	5.000000
+Au	10.000000	0.000000	5.000000
+Hg	11.000000	0.000000	5.000000
+Tl	12.000000	0.000000	5.000000
+Pb	13.000000	0.000000	5.000000
+Bi	14.000000	0.000000	5.000000
+Po	15.000000	0.000000	5.000000
+At	16.000000	0.000000	5.000000
+Rn	17.000000	0.000000	5.000000
+Fr	0.000000	0.000000	6.000000
+Ra	1.000000	0.000000	6.000000
+Ac	2.000000	0.000000	6.000000
+Th	4.000000	0.000000	10.000000
+Pa	5.000000	0.000000	10.000000
+U	6.000000	0.000000	10.000000
+Np	7.000000	0.000000	10.000000
+Pu	8.000000	0.000000	10.000000
+Am	9.000000	0.000000	10.000000
+Cm	10.000000	0.000000	10.000000
+Bk	11.000000	0.000000	10.000000
+Cf	12.000000	0.000000	10.000000
+Es	13.000000	0.000000	10.000000
+Fm	14.000000	0.000000	10.000000
+Md	15.000000	0.000000	10.000000
+No	16.000000	0.000000	10.000000
+Lr	17.000000	0.000000	10.000000
+Rf	3.000000	0.000000	6.000000
+Ha	4.000000	0.000000	6.000000
+Sg	5.000000	0.000000	6.000000
+Ns	6.000000	0.000000	6.000000
+Hs	7.000000	0.000000	6.000000
+Mt	8.000000	0.000000	6.000000
+Ds	9.000000	0.000000	6.000000
+Rg	10.000000	0.000000	6.000000
+Cn	11.000000	0.000000	6.000000
+Nh	12.000000	0.000000	6.000000
+Fl	13.000000	0.000000	6.000000
+Mc	14.000000	0.000000	6.000000
+Lv	15.000000	0.000000	6.000000
+Ts	16.000000	0.000000	6.000000
+Og	17.000000	0.000000	6.000000

proxy/MD-driver/PeriodicTable.cpp

+#include "PeriodicTable.h"
+
+void CreatePeriodicTable (float * atoms, float scaling)
+{
+
+atoms[0]=0; //H
+atoms[1]=0;
+atoms[2]=0;
+atoms[3]=0;
+atoms[4]=17*scaling; //He
+atoms[5]=0;
+atoms[6]=0;
+atoms[7]=1;
+
+int currentAtom=2;
+
+for (int row=1;row<3;row ++) {
+	for (int j=0; j<2;j++) {//left
+		atoms[currentAtom*4]=j*scaling;
+		atoms[currentAtom*4+1]=0;
+		atoms[currentAtom*4+2]=-row*scaling;
+		atoms[currentAtom*4+3]=currentAtom;
+
+		currentAtom++;
+	}
+
+	for (int j=0; j<6;j++) {//right
+		atoms[currentAtom*4]=(j+12)*scaling;
+		atoms[currentAtom*4+1]=0;
+		atoms[currentAtom*4+2]=-row*scaling;
+		atoms[currentAtom*4+3]=currentAtom;
+
+		currentAtom++;
+	}
+
+}
+
+for (int row=3;row<5;row ++) {
+	for (int j=0; j<18;j++) {//left
+		atoms[currentAtom*4]=j*scaling;
+		atoms[currentAtom*4+1]=0;
+		atoms[currentAtom*4+2]=-row*scaling;
+		atoms[currentAtom*4+3]=currentAtom;
+
+		currentAtom++;
+	}
+
+}
+
+for (int row=5;row<7;row ++) {
+	for (int j=0; j<3;j++) {//left
+		atoms[currentAtom*4]=j*scaling;
+		atoms[currentAtom*4+1]=0;
+		atoms[currentAtom*4+2]=-row*scaling;
+		atoms[currentAtom*4+3]=currentAtom;
+
+		currentAtom++;
+	}
+
+	currentAtom+=14;
+
+	for (int j=0; j<15;j++) {//right
+		atoms[currentAtom*4]=(j+3)*scaling;
+		atoms[currentAtom*4+1]=0;
+		atoms[currentAtom*4+2]=-row*scaling;
+		atoms[currentAtom*4+3]=currentAtom;
+
+		currentAtom++;
+	}
+
+}
+
+//rare earths
+currentAtom=57;
+for (int row=0;row<2;row ++) {
+	for (int j=0; j<14;j++) {
+		atoms[currentAtom*4]=(j+4)*scaling;
+		atoms[currentAtom*4+1]=0;
+		atoms[currentAtom*4+2]=(-row-8)*scaling;
+		atoms[currentAtom*4+3]=currentAtom;
+
+		currentAtom++;	
+	}
+	currentAtom=89;
+
+}
+
+}
+

proxy/MD-driver/PeriodicTable.h

+
+void CreatePeriodicTable (float * atoms, float scaling);
+

proxy/MD-driver/PeriodicTableMain.cpp

+#include "NOMADVRLib/ConfigFileAtoms.h"
+#include "NOMADVRLib/atoms.hpp"
+#include "exportXYZ.h"
+#include "PeriodicTable.h"
+
+int main (int argc, char ** argv) 
+{
+
+//create periodic table
+if (argc!=2) {
+	fprintf (stderr, "Required argument, XYZ filename\n");
+	return 1;
+}
+
+numAtoms=new int[1];
+numAtoms[0]=118;
+
+atoms=new float* [1];
+atoms[0]=new float[118*4];
+
+CreatePeriodicTable(atoms[0], 5);
+
+exportXYZ(argv[1], "PeriodicTable", 1);
+
+return 0;
+}
+

proxy/MD-driver/Readme

+Programs:
+PeriodicTable 
+	takes one filename as input and generates an XYZ with the atoms at the standard periodic table positions.
+Simplemove
+	Parameters: <server> <port> <secret>
+	Usage: 
+		Run the program in a shared filesystem folder.
+		The program connects to a NOMADVR proxy server, then generates config and xyz files
+		Other OpenVR NOMADVR instances can use these config files to enable atom Drag-and-drop functionality,
+			using the touchpad in the second controller.
+		The XYZ file in the disk contains the latest atom configuration.
+	
+Simplemove can be used as a sample program to interface OpenVR NOMAD VR with interactive molecular dynamics codes.
+
+Compilation:
+Requires: happyhttp NOMADVRLib rapidjson
+Copy these folders here and run "make".
+
+

proxy/MD-driver/SimpleMove.cpp

+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include <unistd.h>
+#include <sys/types.h>
+#include <sys/socket.h>
+#include <netdb.h>
+
+#include "NOMADVRLib/ConfigFileAtoms.h"
+#include "NOMADVRLib/atoms.hpp"
+#include "PeriodicTable.h"
+#include "exportXYZ.h"
+#include "state.h"
+#include "myrecv.h"
+
+#ifndef INVALID_SOCKET
+#define INVALID_SOCKET -1
+#define closesocket close
+#endif
+
+const int NUMATOMS=118;
+
+int main (int argc, char ** argv)
+{
+
+if (argc!=4) {
+	fprintf (stderr, "Parameters: <server> <port> <secret>\n");
+	return 1;
+}
+
+state_t state;
+
+numAtoms=new int[1];
+numAtoms[0]=NUMATOMS;
+
+atoms=new float* [1];
+atoms[0]=new float[NUMATOMS*4];
+
+CreatePeriodicTable(atoms[0], 5);
+
+exportXYZ("A.xyz", "PeriodicTable", 1);
+
+FILE *ncfg=fopen ("A.ncfg", "w");
+fprintf (ncfg, "xyzfile A.xyz\n"
+	"server %s %s %s\n"
+	"menubutton Infobox\n"
+	"sidebuttontimestep 0\n", argv[1], argv[2], argv[3]);
+fclose (ncfg);
+
+//connect to server, TCP
+
+int sock;
+
+struct hostent *he;
+struct sockaddr_in serv_addr;
+
+	if ( (he = gethostbyname(argv[1]) ) == nullptr ) {
+		fprintf (stderr, "Connect to server, could not get host name %s\n", argv[1]);
+      return 2; /* error */
+	}
+	memset((char *) &serv_addr, 0, sizeof(serv_addr));
+	memcpy(&serv_addr.sin_addr, he->h_addr_list[0], he->h_length);
+	serv_addr.sin_family = AF_INET;
+	serv_addr.sin_port = htons(atoi(argv[2]));
+	sock=socket(AF_INET,SOCK_STREAM,IPPROTO_TCP);
+	if ( connect(sock, (struct sockaddr *)&serv_addr, sizeof(serv_addr))) {
+				fprintf (stderr, "Connect to server, could not get connection %s\n", argv[1]);
+      return 3; /* error */
+	}
+
+int n;
+	int32_t tmp;
+	tmp=htonl (atoi(argv[3])); //secret
+	n = send(sock, (char*)&tmp , sizeof(tmp), 0);
+	if (n<sizeof(tmp)) {
+		closesocket(sock);
+		sock=INVALID_SOCKET;
+		fprintf (stderr, "couldn't send secret\n");
+		return 4;
+	}
+
+
+char buffer[100];
+
+uint32_t ID;
+int found;
+while (true) {
+	n=myrecv(sock, buffer, 1, 0);
+	if (n<1) {
+			fprintf (stderr, "couldn't receive data command");
+			return 5;
+	}
+	printf ("received order %c\n", buffer[0]);
+	switch (buffer[0]) {
+		case 'X': // ID
+		n=myrecv(sock, &ID, 4, 0);
+		if (n<4) {
+			fprintf (stderr, "couldn't receive data X");
+			return 5;
+		}
+		break;
+
+		case 't': 
+		n=myrecv(sock, &state.timestep, 4, 0);
+		if (n<4) 
+{
+			fprintf (stderr, "couldn't receive data t");
+			return 5;
+		}
+		break;
+
+		case 'i':
+		n=myrecv(sock, &state.iso, 4, 0);
+		if (n<4) 
+{
+			fprintf (stderr, "couldn't receive data i\n");
+			return 5;
+		}
+		break;
+
+		case 's': 
+		n=myrecv(sock, &state.showatoms, 1, 0);
+		if (n<1) 
+{
+			fprintf (stderr, "couldn't receive data s\n");
+			return 5;
+		}
+		break;
+
+		case 'n': 
+		n=myrecv(sock, &state.ncfg, 4, 0);
+		if (n<4) 
+{
+			fprintf (stderr, "couldn't receive data n\n");
+			return 5;
+		}
+		break;
+
+		case 'p': // user position
+		n=myrecv (sock, buffer+1, sizeof(float)*3 + 4, 0);
+		if (n<sizeof(float)*3 + 4) {
+			fprintf (stderr, "couldn't receive data p\n");
+			return 5;
+		}
+		break;
+
+		case 'd': //disconnect
+		n=myrecv (sock, buffer+1, 4, 0);
+		if (n<4) 
+{
+			fprintf (stderr, "couldn't receive data d\n");
+			return 5;
+		}
+		break;
+
+		case 'D': //Drag
+		n=myrecv (sock, buffer+1, 6*sizeof(float) + 4*2 +1, 0);
+		if (n<6*sizeof(float) + 4*2 +1) 
+{
+			fprintf (stderr, "couldn't receive data D\n");
+			return 5;
+		}
+		//find the nearest atom
+		//test, use atom 0
+		float orig[3];
+		float dest[3];
+		uint32_t ID, time;
+		char button;
+		memcpy (&ID, buffer+1, 4);
+		memcpy (orig, buffer+5, 3*sizeof(float));
+		memcpy (dest, buffer+5+3*sizeof(float), 3*sizeof(float));
+		memcpy (&time, buffer+5+6*sizeof(float), 4);
+		button=buffer[1+6*sizeof(float)+8];
+		if (button!=2) {
+			printf ("intermediate, discarding\n");
+			continue;
+		}
+		found=-1;
+		for (int i=0;i<NUMATOMS;i++) {
+			float sum=0;
+			for (int j=0;j<3;j++) {
+				const float tmp=atoms[0][i*4+j]-orig[j];
+				sum+=tmp*tmp;
+			}
+			const float r=atomRadius(static_cast<int>(atoms[0][i*4+3]));
+			if (sum < r*r) {
+				found=i;
+				break;
+			}
+			
+		}
+		if (found!=-1) {
+			printf ("Starting Drag atom %d\n", found);
+			//drag it
+			for (int i=0;i<3;i++)
+				atoms[0][found*4+i]+=dest[i]-orig[i];
+
+			exportXYZ("A.xyz", "PeriodicTable", 1);
+			//reload scene
+
+			buffer[0]='n';
+			memcpy(buffer+1, (char*)&state.ncfg, 4);
+			n=send (sock, buffer, 5, 0);
+			if (n<5) {
+				fprintf (stderr, "could not send reload command\n");
+				return 6;
+			}
+			printf ("Reload sent\n");
+		}
+		break;
+
+		default: 
+			fprintf (stderr, "Unknown command received: '%c', %d\n", buffer[0], buffer[0]);
+			return -5;
+	}
+}
+
+return 0;
+}

proxy/MD-driver/eprintf.cpp

+/*
+# Copyright 2016-2018 Ruben Jesus Garcia Hernandez
+#
+# 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>