Adding cfg2x3d for converting cfg files to x3d files for easy viewing.

util/cfg.py

@@ -0,0 +1,58 @@
+import re
+
+def load_array(lines, tuple_length=3, skip=0):
+    regex = r"^([\-eE0-9\.]+)"
+    for i in range(tuple_length+skip-1):
+        regex += r"[ \t]+([\-eE0-9\.]+)"
+    regex += r".*"
+    compiled_regex = re.compile(regex)
+    result = []
+    for line in lines:
+        m = compiled_regex.match(line)
+        if m is not None:
+            r = [float(m.group(i+skip+1)) for i in range(tuple_length)]
+            result.append(tuple(r))
+    return result
+
+def load_cells(cells_filename, coords_filename = None):
+    if coords_filename is None:
+        coords_filename = 'cells-coords.cfg'
+    cells_lines = []
+    coords_lines = []
+    with open(cells_filename) as f:
+        cells_lines += f.readlines()
+    with open(coords_filename) as f:
+        coords_lines += f.readlines()
+    cells_mags = load_array(cells_lines)
+    cells_coords = load_array(coords_lines)
+    assert(len(cells_mags) == len(cells_coords))
+    result = []
+    for i in range(len(cells_mags)):
+        (x, y, z) = cells_coords[i]
+        (u, v, w) = cells_mags[i]
+        result.append((x,y,z,u,v,w))
+    return result
+
+def load_atoms(atoms_filename, coords_filename = None):
+    if coords_filename is None:
+        coords_filename = 'atoms-coords.cfg'
+    atoms_lines = []
+    coords_lines = []
+    with open(atoms_filename) as f:
+        atoms_lines += f.readlines()
+    with open(coords_filename) as f:
+        coords_lines += f.readlines()
+    atoms_mags = load_array(atoms_lines)
+    atoms_coords = load_array(coords_lines, skip=2)
+    assert(len(atoms_mags) == len(atoms_coords))
+    result = []
+    for i in range(len(atoms_mags)):
+        (x, y, z) = atoms_coords[i]
+        (u, v, w) = atoms_mags[i]
+        result.append((x,y,z,u,v,w))
+    return result
+
+
+
+
+

util/cfg2x3d.py

@@ -0,0 +1,125 @@
+import cfg
+import sys
+import math
+
+x3d_atom_template = \
+r"""<Transform translation='{position[0]:f} {position[1]:f} {position[2]:f}'>
+<Transform rotation='0 0 1 {rotation[phi]:f}'> <!--phi-->
+<Transform rotation='0 1 0 {rotation[theta]:f}'> <!--theta-->
+<Transform scale='{scale:f} {scale:f} {scale:f}'>
+<Transform rotation='1 0 0 1.570796325'>
+<Transform scale='0.2 0.2 0.2'>
+<Shape>
+<Appearance>
+<Material diffuseColor='0.7 0.7 0.7' ></Material>
+</Appearance>
+<Sphere></Sphere>
+</Shape>
+</Transform>
+<Transform translation='0 -0.05 0'> <Transform scale='0.075 0.45 0.075'>
+<Shape>
+<Appearance>
+<Material diffuseColor='{color[0]} {color[1]} {color[2]}' ></Material>
+</Appearance>
+<Cylinder></Cylinder>
+</Shape>
+</Transform> </Transform>
+<Transform translation='0 0.4 0'> <Transform scale='0.15 0.1 0.15'>
+<Shape>
+<Appearance>
+<Material diffuseColor='{color[0]} {color[1]} {color[2]}' ></Material>
+</Appearance>
+<Cone></Cone>
+</Shape>
+</Transform> </Transform>
+</Transform>
+</Transform>
+</Transform>
+</Transform>
+</Transform>
+"""
+
+x3d_start_template = \
+r"""<X3D version='3.2' profile='Immersive' xmlns:xsd='http://www.w3.org/2001/XMLSchema-instance' xsd:noNamespaceSchemaLocation='http://www.web3d.org/specifications/x3d-3.2.xsd'>
+<Scene>
+<Viewpoint bind='true' isActive='true' position='{position[0]:f} {position[1]:f} {position[2]:f}' centerOfRotation='{center[0]:f} {center[1]:f} {center[2]:f}'></Viewpoint>
+"""
+
+x3d_end_template = \
+r"""</Scene>
+</X3D>
+"""
+
+def norm(v):
+    return (sum([x*x for x in v]))**0.5
+
+def diff(arr):
+    return [arr[i+1] - arr[i] for i in range(len(arr)-1)]
+
+def main():
+    # get parsers
+    print("EXPERIMENTAL! USE WITH CAUTION! Email yifangu" + "@andrew.cmu.edu for questions.")
+    parsers = {"atoms": cfg.load_atoms, "cells": cfg.load_cells}
+    if len(sys.argv) != 4:
+        print("Usage {:} [{:}] CELLS_OR_ATOMS_DATA_CFG CELLS_OR_ATOMS_COORDS_CFG".format(sys.argv[0], "|".join(parsers)))
+        return -1
+    mode = sys.argv[1]
+    if mode not in parsers:
+        print("{:} is not a valid mode")
+        print("valid modes are {:}".format("|".join(parsers)))
+        return -1
+    filename = sys.argv[2]
+    coords_filename = sys.argv[3]
+    out_filename = filename + ".x3d"
+    print("Processing {:}".format(filename))
+
+    # load data
+    try:
+        data = []
+        for d in parsers[mode](filename, coords_filename):
+            if sum([abs(x) for x in d]) != 0:
+                data.append(d)
+    except Exception as e:
+        print("Error while parsing file. Check selected mode and source files.")
+        return -1
+
+    # preprocess data
+    data_t = list(zip(*data))
+    xyz_sorted = [sorted(arr) for arr in data_t[:3]]
+    mins = [K[0] for K in xyz_sorted]
+    maxs = [K[-1] for K in xyz_sorted]
+    centers = [(a+b)/2.0 for (a,b) in zip(maxs, mins)]
+    dims = [a-b for (a,b) in zip(maxs, mins)]
+    grid_sizes = [max(diff(arr)) for arr in xyz_sorted]
+
+    x3d_start_data = {
+        "center": centers,
+        "position": [centers[0], centers[1], centers[2] + max(dims) * 2.0]
+    }
+
+    # output plt file
+    with open(out_filename, "w") as f:
+        f.write(x3d_start_template.format(**x3d_start_data))
+        for d in data:
+            (x,y,z,u,v,w) = d
+            n = norm(d[3:])
+            if n != 0:
+                color = [(((k/n+1.0)/2.0)) for k in d[3:]]
+                x3d_data = {
+                    "position": (x, y, z),
+                    "rotation": {
+                        "theta":math.atan2((u**2.0+v**2.0)**0.5,w),
+                        "phi":math.atan2(v,u)
+                    },
+                    "scale":0.8*min(grid_sizes),
+                    "color": color
+                }
+                f.write(x3d_atom_template.format(**x3d_data))
+            else:
+                print("Invalid Magnetization! Skipping")
+        f.write(x3d_end_template)
+    print("Done, output {:}".format(out_filename))
+    return 0
+
+if __name__ == '__main__':
+    main()

util/x3dviewer/LICENSE

@@ -0,0 +1,43 @@
+Dual licensed under the MIT and GPL licenses.
+
+==[MIT]====================================================================
+Copyright (c) 2009 X3DOM
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+
+==[GPL]====================================================================
+
+X3DOM - Declarative 3D for HTML
+
+Copyright (C) 2009 X3DOM
+
+This program is free software: you can redistribute it and/or modify   
+it under the terms of the GNU General Public License as published by   
+the Free Software Foundation, either version 3 of the License, or      
+(at your option) any later version.                                    
+
+This program is distributed in the hope that it will be useful,        
+but WITHOUT ANY WARRANTY; without even the implied warranty of         
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the          
+GNU General Public License for more details.                           
+
+You should have received a copy of the GNU General Public License      
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+