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Commit 99c5d0b0 authored by Ruben Jesus Garcia Hernandez's avatar Ruben Jesus Garcia Hernandez
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Removed files which are now in the nomad vr lib

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OculusMobile/readme.md 0 → 100644
View file @ 99c5d0b0
This repository contains the demos for GearVR using Oculus Mobile version 1.0.0.0
https://developer3.oculus.com/documentation/mobilesdk/latest/
Clone that repository and add the content of this one inside the VrSamples\Native directory.
Copy the content of the ../libs directory (rply, happyhttp, rapidjson) into NOMADGearvrT\Src
List of directories
NOMADGearvrT:
This program can load prepared molecular dynamics simulations, and is
compatible with the TimestepData OpenVR demo.
Ply support is not yet implemented
\ No newline at end of file
OpenVR/TimestepData/TessShaders.cpp deleted 100644 → 0
View file @ 15f4da94
#include "TessShaders.h"
/*rgh: for now default tesselation control, using
glPatchParameterfv(GL_PATCH_DEFAULT_OUTER_LEVEL, {3,3,3,3});
glPatchParameterfv(GL_PATCH_DEFAULT_INNER_LEVEL, {3,3});
*/
const char * const AtomShaders [] = {
"Atom Renderer",
// vertex shader
"#version 410\n"
"uniform sampler2D atomData;\n"
"layout(location = 0) in vec3 center;\n"
"layout(location = 1) in float atomIn;\n"
"out vec4 vcolor;\n" //color , radius
"out vec3 vcen;"
"void main()\n"
"{\n"
//"gl_Position = matrix * vec4(position+center, 1);\n"
"float coord=atomIn/118.0+0.5/118.0;\n"
"vcolor=vec4(texture(atomData, vec2(coord, 0)));\n"
"vcen=center;\n"
//"color.a=1;\n"
"}\n",
//fragment shader
"#version 410 core\n"
"in vec4 color;\n"
"in vec3 vertex;"
"in vec3 normal;"
"out vec4 outputColor;\n"
"void main()\n"
"{\n"
//"vec3 U = dFdx(vertex); "
//"vec3 V = dFdy(vertex); "
"vec3 nn = normalize(normal);"
//"vec3 nn = normalize(cross(U,V));"
"lowp float a=abs(dot(nn, vec3(0,sqrt(2.0)/2.0,sqrt(2.0)/2.0)));\n"
"lowp float b=max(0.0, dot(nn, vec3(0,0,1)));\n"
"highp vec4 res=color;\n"
" outputColor = vec4 ((res.rgb) * (0.1 + 0.2*a), color.a);\n"
"}\n",
//tess eval
"#version 400\n"
//"layout(triangles, equal_spacing, cw) in;\n"
"layout(quads, equal_spacing, cw) in;\n"
"#define pi 3.1415926535897932384626433832795\n"
"uniform mat4 matrix;\n"
//"uniform mat4 mv;\n"
"in vec4 vcolor[];\n" //color , radius
"in vec3 vcen[];"
"out vec4 color;\n" //color
"out vec3 normal;\n"
"out vec3 vertex;"
"uniform mat4 Projection;\n"
"uniform mat4 Modelview;\n"
"void main()\n"
"{\n"
"normal=vec3(sin(gl_TessCoord.x*2*pi)*cos((gl_TessCoord.y-0.5)*pi), "
"cos(gl_TessCoord.x*2*pi)*cos((gl_TessCoord.y-0.5)*pi), "
"sin((gl_TessCoord.y-0.5)*pi));"
" vertex = normal * vcolor[0].w + vcen[0];\n"
"color=vec4(vcolor[0].xyz, 1);"
"gl_Position = matrix * vec4(vertex, 1);\n"
"}\n"
};
\ No newline at end of file
OpenVR/TimestepData/TessShaders.h deleted 100644 → 0
View file @ 15f4da94
#define SHADERNAME 0
#define SHADERVERTEX 1
#define SHADERFRAGMENT 2
#define SHADERTESSEVAL 3
extern const char * const AtomShaders[];
\ No newline at end of file
OpenVR/TimestepData/UnitCellShaders.cpp deleted 100644 → 0
View file @ 15f4da94
#include "UnitCellShaders.h"
const char * const UnitCellShaders [] = {"Unit Cell Renderer",
//vertex
"#version 410\n"
"uniform mat4 matrix;\n"
"layout(location = 0) in vec3 pos;\n"
"void main()\n"
"{\n"
"gl_Position = matrix * vec4(pos, 1);\n"
"}\n"
,
//fragment
"#version 410 core\n"
"uniform vec4 color;\n"
"out vec4 outputColor;\n"
"void main()\n"
"{\n"
" outputColor = color;\n"
"}\n"
,
//tess
nullptr
};
OpenVR/TimestepData/UnitCellShaders.h deleted 100644 → 0
View file @ 15f4da94
extern const char * const UnitCellShaders[];
\ No newline at end of file
OpenVR/TimestepData/atoms.cpp deleted 100644 → 0
View file @ 15f4da94
#define NOMINMAX
#include <stdio.h>
#include <string.h>
#include <vector>
#include <winsock2.h>
#include "atoms.hpp"
#include "rapidjson/document.h"
#include "rapidjson/filereadstream.h"
#include "happyhttp.h"
const char * const atomNames[] =
{
"H", "He",
"Li", "Be", "B", "C", "N", "O", "F", "Ne",
"Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar",
"K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr",
"Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe",
"Cs", "Ba",
"La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu",
"Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn",
"Fr", "Ra",
"Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr",
"Rf", "Ha", "Sg", "Ns", "Hs", "Mt", "Ds", "Rg", "Cn", "Nh", "Fl", "Mc", "Lv", "Ts", "Og"
};
//rgb radius for easy transfer to texture. In AAngstrom
//not const as users may want to scale the radius
float atomColours[][4] =
{
{1.000000f, 1.000000f, 1.000000f, 0.310000f},//H
{0.851000f, 1.000000f, 1.000000f, 0.280000f},//He
{0.800000f, 0.502000f, 1.000000f, 1.280000f},//Li
{0.761000f, 1.000000f, 0.000000f, 0.960000f},//Be
{1.000000f, 0.710000f, 0.710000f, 0.840000f},//B
{0.565000f, 0.565000f, 0.565000f, 0.760000f},//C
{0.188000f, 0.314000f, 0.973000f, 0.710000f},//N
{1.000000f, 0.051000f, 0.051000f, 0.660000f},//O
{0.565000f, 0.878000f, 0.314000f, 0.570000f},//F
{0.702000f, 0.890000f, 0.961000f, 0.580000f},//Ne
{0.671000f, 0.361000f, 0.949000f, 1.660000f},//Na
{0.541000f, 1.000000f, 0.000000f, 1.410000f},//Mg
{0.749000f, 0.651000f, 0.651000f, 1.210000f},//Al
{0.941000f, 0.784000f, 0.627000f, 1.110000f},//Si
{1.000000f, 0.502000f, 0.000000f, 1.070000f},//P
{1.000000f, 1.000000f, 0.188000f, 1.050000f},//S
{0.122000f, 0.941000f, 0.122000f, 1.020000f},//Cl
{0.502000f, 0.820000f, 0.890000f, 1.060000f},//Ar
{0.561000f, 0.251000f, 0.831000f, 2.030000f},//K
{0.239000f, 1.000000f, 0.000000f, 1.760000f},//Ca
{0.902000f, 0.902000f, 0.902000f, 1.700000f},//Sc
{0.749000f, 0.761000f, 0.780000f, 1.600000f},//Ti
{0.651000f, 0.651000f, 0.671000f, 1.530000f},//V
{0.541000f, 0.600000f, 0.780000f, 1.390000f},//Cr
{0.612000f, 0.478000f, 0.780000f, 1.390000f},//Mn
{0.878000f, 0.400000f, 0.200000f, 1.320000f},//Fe
{0.941000f, 0.565000f, 0.627000f, 1.260000f},//Co
{0.314000f, 0.816000f, 0.314000f, 1.240000f},//Ni
{0.784000f, 0.502000f, 0.200000f, 1.320000f},//Cu
{0.490000f, 0.502000f, 0.690000f, 1.220000f},//Zn
{0.761000f, 0.561000f, 0.561000f, 1.220000f},//Ga
{0.400000f, 0.561000f, 0.561000f, 1.200000f},//Ge
{0.741000f, 0.502000f, 0.890000f, 1.190000f},//As
{1.000000f, 0.631000f, 0.000000f, 1.200000f},//Se
{0.651000f, 0.161000f, 0.161000f, 1.200000f},//Br
{0.361000f, 0.722000f, 0.820000f, 1.160000f},//Kr
{0.439000f, 0.180000f, 0.690000f, 2.200000f},//Rb
{0.000000f, 1.000000f, 0.000000f, 1.950000f},//Sr
{0.580000f, 1.000000f, 1.000000f, 1.900000f},//Y
{0.580000f, 0.878000f, 0.878000f, 1.750000f},//Zr
{0.451000f, 0.761000f, 0.788000f, 1.640000f},//Nb
{0.329000f, 0.710000f, 0.710000f, 1.540000f},//Mo
{0.231000f, 0.620000f, 0.620000f, 1.470000f},//Tc
{0.141000f, 0.561000f, 0.561000f, 1.460000f},//Ru
{0.039000f, 0.490000f, 0.549000f, 1.420000f},//Rh
{0.000000f, 0.412000f, 0.522000f, 1.390000f},//Pd
{0.753000f, 0.753000f, 0.753000f, 1.450000f},//Ag
{1.000000f, 0.851000f, 0.561000f, 1.440000f},//Cd
{0.651000f, 0.459000f, 0.451000f, 1.420000f},//In
{0.400000f, 0.502000f, 0.502000f, 1.390000f},//Sn
{0.620000f, 0.388000f, 0.710000f, 1.390000f},//Sb
{0.831000f, 0.478000f, 0.000000f, 1.380000f},//Te
{0.580000f, 0.000000f, 0.580000f, 1.390000f},//I
{0.259000f, 0.620000f, 0.690000f, 1.400000f},//Xe
{0.341000f, 0.090000f, 0.561000f, 2.440000f},//Cs
{0.000000f, 0.788000f, 0.000000f, 2.150000f},//Ba
{0.439000f, 0.831000f, 1.000000f, 2.070000f},//La
{1.000000f, 1.000000f, 0.780000f, 2.040000f},//Ce
{0.851000f, 1.000000f, 0.780000f, 2.030000f},//Pr
{0.780000f, 1.000000f, 0.780000f, 2.010000f},//Nd
{0.639000f, 1.000000f, 0.780000f, 1.990000f},//Pm
{0.561000f, 1.000000f, 0.780000f, 1.980000f},//Sm
{0.380000f, 1.000000f, 0.780000f, 1.980000f},//Eu
{0.271000f, 1.000000f, 0.780000f, 1.960000f},//Gd
{0.188000f, 1.000000f, 0.780000f, 1.940000f},//Tb
{0.122000f, 1.000000f, 0.780000f, 1.920000f},//Dy
{0.000000f, 1.000000f, 0.612000f, 1.920000f},//Ho
{0.000000f, 0.902000f, 0.459000f, 1.890000f},//Er
{0.000000f, 0.831000f, 0.322000f, 1.900000f},//Tm
{0.000000f, 0.749000f, 0.220000f, 1.870000f},//Yb
{0.000000f, 0.671000f, 0.141000f, 1.870000f},//Lu
{0.302000f, 0.761000f, 1.000000f, 1.750000f},//Hf
{0.302000f, 0.651000f, 1.000000f, 1.700000f},//Ta
{0.129000f, 0.580000f, 0.839000f, 1.620000f},//W
{0.149000f, 0.490000f, 0.671000f, 1.510000f},//Re
{0.149000f, 0.400000f, 0.588000f, 1.440000f},//Os
{0.090000f, 0.329000f, 0.529000f, 1.410000f},//Ir
{0.816000f, 0.816000f, 0.878000f, 1.360000f},//Pt
{1.000000f, 0.820000f, 0.137000f, 1.360000f},//Au
{0.722000f, 0.722000f, 0.816000f, 1.320000f},//Hg
{0.651000f, 0.329000f, 0.302000f, 1.450000f},//Tl
{0.341000f, 0.349000f, 0.380000f, 1.460000f},//Pb
{0.620000f, 0.310000f, 0.710000f, 1.480000f},//Bi
{0.671000f, 0.361000f, 0.000000f, 1.400000f},//Po
{0.459000f, 0.310000f, 0.271000f, 1.500000f},//At
{0.259000f, 0.510000f, 0.588000f, 1.500000f},//Rn
{0.259000f, 0.000000f, 0.400000f, 2.600000f},//Fr
{0.000000f, 0.490000f, 0.000000f, 2.210000f},//Ra
{0.439000f, 0.671000f, 0.980000f, 2.150000f},//Ac
{0.000000f, 0.729000f, 1.000000f, 2.060000f},//Th
{0.000000f, 0.631000f, 1.000000f, 2.000000f},//Pa
{0.000000f, 0.561000f, 1.000000f, 1.960000f},//U
{0.000000f, 0.502000f, 1.000000f, 1.900000f},//Np
{0.000000f, 0.420000f, 1.000000f, 1.870000f},//Pu
{0.329000f, 0.361000f, 0.949000f, 1.800000f},//Am
{0.471000f, 0.361000f, 0.890000f, 1.690000f},//Cm
{0.541000f, 0.310000f, 0.890000f, MISSINGRADIUS},//Bk
{0.631000f, 0.212000f, 0.831000f, MISSINGRADIUS},//Cf
{0.702000f, 0.122000f, 0.831000f, MISSINGRADIUS},//Es
{0.702000f, 0.122000f, 0.729000f, MISSINGRADIUS},//Fm
{0.702000f, 0.051000f, 0.651000f, MISSINGRADIUS},//Md
{0.741000f, 0.051000f, 0.529000f, MISSINGRADIUS},//No
{0.780000f, 0.000000f, 0.400000f, MISSINGRADIUS},//Lr
{0.800000f, 0.000000f, 0.349000f, MISSINGRADIUS},//Rf
{0.820000f, 0.000000f, 0.310000f, MISSINGRADIUS},//Ha
{0.851000f, 0.000000f, 0.271000f, MISSINGRADIUS},//Sg
{0.878000f, 0.000000f, 0.220000f, MISSINGRADIUS},//Ns
{0.902000f, 0.000000f, 0.180000f, MISSINGRADIUS},//Hs
{0.922000f, 0.000000f, 0.149000f, MISSINGRADIUS},//Mt
{MISSINGR, MISSINGG, MISSINGB, MISSINGRADIUS},//Ds
{MISSINGR, MISSINGG, MISSINGB, MISSINGRADIUS},//Rg
{MISSINGR, MISSINGG, MISSINGB, MISSINGRADIUS},//Cn
{MISSINGR, MISSINGG, MISSINGB, MISSINGRADIUS},//Nh
{MISSINGR, MISSINGG, MISSINGB, MISSINGRADIUS},//Fl
{MISSINGR, MISSINGG, MISSINGB, MISSINGRADIUS},//Mc
{MISSINGR, MISSINGG, MISSINGB, MISSINGRADIUS},//Lv
{MISSINGR, MISSINGG, MISSINGB, MISSINGRADIUS},//Ts
{MISSINGR, MISSINGG, MISSINGB, MISSINGRADIUS},//Og
};
void discardline (FILE *F)
{
int c;
do {
c = fgetc(F);
} while (c != EOF && c != '\n');
}
int findAtom(const char *const s)
{
//rgh FIXME, add caching
for (int i=0;i<sizeof(atomNames)/sizeof(const char *);i++)
if (!strcmp(s, atomNames[i]))
return i;
return -1;
}
char * readAtomsXYZErrors[] = {
"All Ok",//0
"could not open file", //-1
"error loading atom type and position line", //-2
"atom type unknown", //-3
};
int readAtomsXYZ(const char *const file, int **numatoms, int *timesteps, float ***pos)
{
int mynumatoms;
std::vector<float*> mypos;
std::vector<int> mynum;
FILE *f=fopen (file, "r");
int r;
char s[100];
if (f==0)
return -1;
*timesteps=0;
while (!feof(f)) {
r=fscanf(f, "%d", &mynumatoms);
if (r<1)
continue; //there may be a blank line at the end of the file
(*timesteps)++;
discardline (f);
mypos.push_back(new float[mynumatoms*4]);
mynum.push_back(mynumatoms);
discardline (f); //comment
for (int i=0;i<mynumatoms;i++) {
r=fscanf (f, "%s %f %f %f", s, mypos.back()+4*i+0, mypos.back()+4*i+1,mypos.back()+4*i+2);
if (r<4)
return -2;
int a=findAtom(s);
if (a==-1)
return -3;
(mypos.back())[4*i+3]=a;
}
}
*pos=new float*[*timesteps];
*numatoms=new int[*timesteps];
for (int i=0;i<*timesteps;i++) {
(*pos)[i]=mypos[i];
(*numatoms)[i]=mynum[i];
}
return 0;
}
char * readAtomsCubeErrors [] ={
"All Ok", //0
"could not open file", //-1
"could not read number of atoms or translation", //-2
"could not read voxel size or unit cell", //-3
"error loading atom type and position line", //-4
};
//We will use Angstrom, convert from bohr if needed
//rgh FIXME, untested code
int readAtomsCube(const char *const file, int **numatoms, int *timesteps, float ***pos)
{
float isoTrans[3];
int voxelSize[3];
float abc[9];
FILE *f = fopen(file, "r");
int r;
if (f == 0)
return -1;
*timesteps = 1;
*pos = new float*[*timesteps];
*numatoms = new int[*timesteps];
discardline(f); //two comments
discardline(f);
r = fscanf(f, "%d %f %f %f", *numatoms, isoTrans + 0, isoTrans + 1, isoTrans + 2);
if (r < 4)
return -2;
**pos = new float[4 * **numatoms];
for (int i = 0; i < 3; i++) {
r = fscanf(f, "%d %f %f %f", voxelSize+i, abc + 0 + 3 * i, abc + 1 + 3 * i, abc + 2 + 3 * i);
if (r < 4)
return -3;
//positive then the units are Bohr, if negative then Angstroms.
if (voxelSize[i] < 0)
voxelSize[i] = -voxelSize[i];
else {
for (int j = 0; j < 3; j++)
abc[j + 3 * i] *= 0.52918;
}
}
for (int i = 0; i < **numatoms; i++) {
int a;
float unused;
r = fscanf(f, "%d %f %f %f %f", &a, &unused, &((**pos)[4 * i + 0]), &((**pos)[4 * i + 1]), &((**pos)[4 * i + 2]));
if (r < 5)
return -4;
(**pos)[4 * i + 3] = a - 1;
}
//rgh FIXME, discard the volumetric data for now
fclose(f);
return 0;
}
FILE *out;
void OnData( const happyhttp::Response* r, void* userdata, const unsigned char* data, int n )
{
fwrite( data,1,n, out );
}
char * readAtomsJsonErrors[] = {
"All Ok",//0
"could not open file", //-1
"error parsing json", //-2
"error downloading json", //-3
};
int readAtomsJsonURL (const char *const f, int **numatoms, int *timesteps, float ***pos, float abc[3][3],
std::vector<float>** clonedAtoms)
{
try {
char host[2048], page[2048], url[2048];
int port=80;
int r;
//http://stackoverflow.com/questions/726122/best-ways-of-parsing-a-url-using-c
r=sscanf (f, "http://%2047[^/:]:%d%2047[^\n]", host, &port, page);
if (r==1)
r=sscanf (f, "http://%2047[^/]%2047[^\n]", host, page);
if (r<2) { //possibly https or other unsupported protocol, fall back to wget
return readAtomsJsonURLwget (f, numatoms, timesteps, pos, abc, clonedAtoms);
}
sprintf (url, "%s%s", page, "/cells");
out=fopen("material_cells.json", "w");
happyhttp::Connection conn( host, port );
conn.setcallbacks( nullptr, OnData, nullptr, 0 );
conn.request( "GET", url, 0, 0,0 );
while( conn.outstanding() )
conn.pump();
fclose(out);
conn.close();
sprintf (url, "%s%s", page, "/elements");
out=fopen("material_elements.json", "w");
conn.request( "GET", url, 0, 0,0 );
while( conn.outstanding() )
conn.pump();
fclose(out);
} catch (const happyhttp::Wobbly& w) {
int e= WSAGetLastError();
fprintf (stderr, "error %d\n", e);
return -3;
}
fclose(out);
//sprintf (cmd, "wget %s/cells -O material_cells.json", f);
//system(cmd);
//sprintf (cmd, "wget %s/elements -O material_elements.json", f);
//system(cmd);
return readAtomsJson ("material", numatoms, timesteps, pos, abc, clonedAtoms);
}
int readAtomsJsonURLwget (const char *const f, int **numatoms, int *timesteps, float ***pos, float abc[3][3],
std::vector<float>** clonedAtoms)
{
char cmd[2048];
int ret;
sprintf (cmd, "wget %s/cells -O material_cells.json", f);
ret=system(cmd);
if (ret!=0)
return (-3);
sprintf (cmd, "wget %s/elements -O material_elements.json", f);
ret=system(cmd);
return(-3);
return readAtomsJson ("material", numatoms, timesteps, pos, abc, clonedAtoms);
}
bool isAlmostZero(float coordinate)
{
return (coordinate < 1E-5);
}
void add (std::vector<float> *v, float x, float y, float z, float a)
{
v->push_back(x);
v->push_back(y);
v->push_back(z);
v->push_back(a);
}
int readAtomsJson (const char *const f, int **numatoms, int *timesteps, float ***pos, float abc[3][3],
std::vector<float>** clonedAtoms)
{
char file[512];
int r;
sprintf (file, "%s_cells.json", f);
FILE *fcells=fopen (file, "r");
if (fcells==0)
return -1;
char readBuffer[65536];
rapidjson::FileReadStream is(fcells, readBuffer, sizeof(readBuffer));
rapidjson::Document json;
json.ParseStream(is);
fclose(fcells);
int total_results=json["total_results"].GetInt();
const rapidjson::GenericValue<rapidjson::UTF8<> > &results=json["results"];
for (int i=0;i<total_results;i++) {
const rapidjson::GenericValue<rapidjson::UTF8<> > &result=results[i];
if (result["is_primitive"].GetBool()==false)
continue;
const char *myabc[3]={result["a"].GetString(), result["b"].GetString(), result["c"].GetString()};
for (int j=0;j<3;j++) {
r=sscanf(myabc[j], "(%f,%f,%f)", &(abc[j][0]), &(abc[j][1]), &(abc[j][2]));
for (int k=0;k<3;k++)
abc[j][k]*=1e10; //using angstrom internally
}
}
sprintf (file, "%s_elements.json", f);
FILE *felements=fopen (file, "r");
if (felements==0)
return -1;
rapidjson::FileReadStream is2(felements, readBuffer, sizeof(readBuffer));
json.ParseStream(is2);
fclose(felements);
*timesteps=1;
*pos = new float*[*timesteps];
*numatoms = new int[*timesteps];
**numatoms=json["total_results"].GetInt();
**pos=new float[4* **numatoms];
*clonedAtoms=new std::vector<float>[*timesteps];
const rapidjson::GenericValue<rapidjson::UTF8<> >& a = json["results"];
float tmppos[3];
for (int i=0;i< **numatoms;i++)
{
const rapidjson::GenericValue<rapidjson::UTF8<> > &result=a[i];
const rapidjson::GenericValue<rapidjson::UTF8<> > &label=result["label"];
if (!label.IsInt())
return -2;
int k=label.GetInt();
(**pos)[4*i + 3]=k;
const char *stringpos=result["position"].GetString();
r=sscanf(stringpos, "(%f,%f,%f)", tmppos+0, tmppos+1, tmppos+2);
//clone
//https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/blob/lauri_viz/viztools/structure/src/typescript/structureviewer.ts
Clone (tmppos, k, *clonedAtoms);
//atom positions in the abc domain, must multiply.
for (int s=0;s<3;s++)
(**pos)[4*i+s]=tmppos[0]*abc[0][s]+tmppos[1]*abc[1][s]+tmppos[2]*abc[2][s];
}
TransformAtoms(*clonedAtoms, abc);
return 0;
}
void TransformAtoms(std::vector<float>* clonedAtoms, const float abc[3][3])
{
float tmppos[3];
for (int o=0;o<clonedAtoms->size()/4;o++) {
for (int s=0;s<3;s++)
tmppos[s]=(*clonedAtoms)[o*4+s];
for (int s=0;s<3;s++)
(*clonedAtoms)[o*4+s]=tmppos[0]*abc[0][s]+tmppos[1]*abc[1][s]+tmppos[2]*abc[2][s];
}
}
void Clone (float tmppos[3], float k, std::vector<float>* clonedAtoms)
{
bool iaz[3];
for (int q=0;q<3;q++)
iaz[q]=isAlmostZero(tmppos[q]);
if (iaz[0] && iaz[1] &&iaz[2]){
add(clonedAtoms, 0,0,1, k);
add(clonedAtoms, 0,1,0, k);
add(clonedAtoms, 0,1,1, k);
add(