align

lib/align.py

@@ -0,0 +1,39 @@
+"""
+Calculated Rotation Matrix to align Vector A to Vector B in 3d using
+Rodrigues' rotation formula.
+
+octave code:
+v1 = [1 1 1]';
+v2 = [0 0 1]';
+w = cross(v1,v2);
+w = w/norm(w);
+w_hat = [0,-w(3),w(2);w(3),0,-w(1);-w(2),w(1),0];
+cos_tht = v1'*v2/norm(v1)/norm(v2);
+tht = acos(cos_tht);
+R = eye(size(v1,1)) + w_hat*sin(tht) + w_hat^2*(1-cos(tht));
+t1 = R*v1;
+t1 = t1/norm(t1)*norm(v2);
+
+"""
+import math
+import numpy as np
+
+def align_axis(v1, v2):
+    w = np.cross(v1,v2)
+    w = w/np.linalg.norm(w)
+    w_hat = np.matrix([[    0, -w[2],  w[1]], 
+                       [ w[2],     0, -w[0]],
+                       [-w[1],  w[0],     0]])
+    cos_tht = np.dot(v1, v2)/np.linalg.norm(v1)/np.linalg.norm(v2)
+    tht = np.arccos(cos_tht)
+    R = np.identity(3) + w_hat*np.sin(tht) + w_hat*w_hat*(1-np.cos(tht))
+    return R
+
+def test():
+    v1 = np.array([1.0, 1.0, 1.0])
+    v2 = np.array([0.0, 0.0, 1.0])
+    R = align_axis(v1, v2)
+    print R
+
+if __name__ == "__main__":
+    test()

tools/vasp/get_potcar.py

@@ -32,7 +32,7 @@
         "Br":"Br", "D": "H", "Si": "Si", "Ni": "Ni", "Pt":"Pt_pv", "Co":"Co", "Cr":"Cr", 
        "I":"I", "K":"K_pv", "F":"F", "W":"W", "Au":"Au", "Cs":"Cs_sv", "Mg":"Mg",
        "Ag":"Ag", "Se":"Se", "B":"B", "He":"He", "Ar":"Ar", "Xe":"Xe", "Kr":"Kr", 
-       "Mo": "Mo",}
+       "Mo": "Mo", "Fe": "Fe",}
 
 if socket.gethostname() == "cluster.hpc.org":
     POT_DATA_BASE = "/project/source/VASP/vasp.5.3.5/potcar/potpaw_PBE"