Periodic table: properties.

src/soap/soapy/CMakeLists.txt

-install(FILES __init__.py util.py npthreads.py kernel.py simspace.py pca.py dimred.py lagraph.py lamatch.py math.py DESTINATION ${LOCAL_INSTALL_DIR}/soapy)
+install(FILES __init__.py elements.py util.py npthreads.py kernel.py simspace.py pca.py dimred.py lagraph.py lamatch.py math.py DESTINATION ${LOCAL_INSTALL_DIR}/soapy)
 

src/soap/soapy/__init__.py

@@ -4,4 +4,5 @@ from dimred import *
 from pca import *
 from util import *
 from math import *
+from elements import *
 

src/soap/soapy/elements.py

+
+
+class PeriodicTable(object):
+    element_elneg = [ 0.0, 
+    2.3, 4.16, 
+    0.912, 1.576, 2.051, 2.544, 3.066, 3.610, 4.193, 4.789,
+    0.869, 1.293, 1.613, 1.916, 2.253, 2.589, 2.869, 3.242,
+    0.734, 1.034, 1.19, 1.38, 1.53, 1.65, 1.75, 1.80, 1.84, 1.88, 1.85, 1.59, 1.756, 1.994, 2.211, 2.434, 2.689, 2.966,
+    0.706, 0.963, 1.12, 1.32, 1.41, 1.47, 1.51, 1.54, 1.56, 1.59, 1.87, 1.52, 1.656, 1.824, 1.984, 2.158, 2.359, 2.582,
+    0.659, 0.881,    
+    0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, # Lanthanides     
+    1.16, 1.34, 1.47, 1.60, 1.65, 1.68, 1.72, 1.92, 1.76, 1.789, 1.854, 2.01,  2.19,  2.39,  2.60,
+    0.67,  0.90,    
+    0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, # Actinides
+    0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+    ] # Allen scale
+    
+    element_names = ["?",
+   "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 ","Db ","Sg ","Bh ","Hs ","Mt ","Ds ","Rg ","Uub", "Uut","Uuq","Uup","Uuh" ]
+
+    element_mass = [-1., 
+1.00794, 4.00260, 6.941, 9.012187, 10.811, 12.0107, 14.00674, 15.9994, 18.99840, 20.1797, 22.98977,  
+24.3050, 26.98154, 28.0855, 30.97376, 32.066, 35.4527, 39.948, 39.0983, 40.078, 44.95591, 47.867,      
+50.9415, 51.9961, 54.93805, 55.845, 58.93320, 58.6934, 63.546, 65.39, 69.723, 72.61, 74.92160, 78.96,  
+79.904, 83.80, 85.4678, 87.62, 88.90585, 91.224, 92.90638, 95.94, 98.0, 101.07, 102.90550, 106.42,     
+107.8682, 112.411, 114.818, 118.710, 121.760, 127.60, 126.90447, 131.29, 132.90545, 137.327, 138.9055, 
+140.116, 140.90765, 144.24, 145.0, 150.36, 151.964, 157.25, 158.92534, 162.50, 164.93032, 167.26,      
+168.93421, 173.04, 174.967, 178.49, 180.9479, 183.84, 186.207, 190.23, 192.217, 195.078, 196.96655,    
+200.59, 204.3833, 207.2, 208.98038, 209.0, 210.0, 222.0, 223.0, 226.0, 227.0, 232.0381, 231.03588,     
+238.0289, 237.0, 244.0, 243.0, 247.0, 247.0, 251.0, 252.0, 257.0, 258.0, 259.0, 262.0, 261.0, 262.0,   
+263.0, 264.0, 265.0, 268.0, 271.0, 272.0, 285.0, 284.0, 289.0, 288.0, 292.0 ]
+
+    element_covrad = [-1.,
+0.320,0.310,1.630,0.900,0.820,0.770,0.750,0.730,0.720,0.710,1.540,1.360,1.180,1.110,1.060,1.020,     
+0.990,0.980,2.030,1.740,1.440,1.320,1.220,1.180,1.170,1.170,1.160,1.150,1.170,1.250,1.260,1.220,1.200, 
+1.160,1.140,1.120,2.160,1.910,1.620,1.450,1.340,1.300,1.270,1.250,1.250,1.280,1.340,1.480,1.440,1.410, 
+1.400,1.360,1.330,1.310,2.350,1.980,1.690,1.650,1.650,1.840,1.630,1.620,1.850,1.610,1.590,1.590,1.580, 
+1.570,1.560,2.000,1.560,1.440,1.340,1.300,1.280,1.260,1.270,1.300,1.340,1.490,1.480,1.470,1.460,1.460, 
+2.000,2.000,2.000,2.000,2.000,1.650,2.000,1.420,2.000,2.000,2.000,2.000,2.000,2.000,2.000,2.000,2.000, 
+2.000,2.000,2.000,2.000,2.000,2.000,2.000,2.000,2.000,2.000,2.000,2.000,2.000,2.000,2.000 ]
+    def __init__(self):
+        self.elements_by_z = {}
+        self.elements_by_name = {}
+    def __getitem__(self, key):
+        if type(key) == str:
+            return self.elements_by_name[key]
+        elif type(key) == int:
+            return self.elements_by_z[key]
+        else:
+            raise RuntimeError("Invalid element identifier '%s'" % key)
+    def setup(self):
+        element_z = [ i for i in range(len(self.element_names)) ]
+        assert len(self.element_names) == len(self.element_mass) == len(self.element_covrad)
+        for z, name, mass, covrad, elneg in zip(element_z, self.element_names, self.element_mass, self.element_covrad, self.element_elneg):
+            name = name.strip()
+            self.addElement(z, name, mass, covrad, elneg)
+        return self
+    def addElement(self, z, name, mass, covrad, elneg):
+        elem = AtomicElement(z, name, mass, covrad, elneg)
+        self.elements_by_z[z] = elem
+        self.elements_by_name[name] = elem
+        return
+    def getPropertyDict(self, key, convert = lambda v: v):
+        props = {}
+        for name, elem in self.elements_by_name.items():
+            props[name] = convert(elem[key])
+        return props
+
+class AtomicElement(object):
+    def __init__(self, z, name, mass, covrad, elneg):
+        self.z = z
+        self.name = name
+        self.mass = mass
+        self.covrad = covrad
+        self.elneg = elneg
+        self.property_dict = { 'z' : z, 'covrad' : covrad, 'name': name, 'mass': mass, 'elneg': elneg }
+    def __getitem__(self, key):
+        return self.property_dict[key]
+
+periodic_table = PeriodicTable().setup()
+
+if __name__ == "__main__":
+    print periodic_table["H"].mass
+    print periodic_table[6].mass
+    print periodic_table[6].covrad
+    print len(periodic_table.element_elneg)
+    print len(periodic_table.element_names)
+    
+    for elem in PeriodicTable.element_names:
+        print elem, periodic_table[elem.strip()]["elneg"]
+    

src/soap/spectrum.cpp

@@ -139,7 +139,7 @@ AtomicSpectrum *Spectrum::computeAtomic(Particle *center, Structure::particle_ar
             weight0 *= _basis->getCutoff()->getCenterWeight();
         }
 
-        GLOG() << "C " << dr.getX() << " " << dr.getY() << " " << dr.getZ() << std::endl;
+        GLOG() << (*pit)->getType() << " " << dr.getX() << " " << dr.getY() << " " << dr.getZ() << std::endl;
 
         // COMPUTE EXPANSION & ADD TO SPECTRUM
         bool gradients = (is_image) ? false : _options->get<bool>("spectrum.gradients");

src/soap/tools/loadwrite.py

@@ -83,6 +83,14 @@ def setup_structure_ase(label, ase_config, top=None):
                 atom_idx += 1
     return structure 
 
+def setup_structure_density(structure, radius_map, charge_map, anonymize=False):
+    for particle in structure:
+        particle.weight = charge_map[particle.type]
+        particle.sigma = radius_map[particle.type]
+        if anonymize:
+            particle.type = "X"
+    return
+
 class AseConfigList(object):
     def __init__(self,
         config_files=[],