Radial basis ticks.

.gitignore

 apply
 build
-./soap
+soap
 Makefile
 test/old
 test/back
@@ -10,3 +10,83 @@ test/back
 *.cube
 *.arch
 *.back
+
+clean.sh
+cxx_tests/load.gp
+cxx_tests/soap_tests/
+cxx_tests/src/gtest_options.py
+cxx_tests/src/soap
+cxx_tests/tmp
+cxx_tests/tmp_basis
+cxx_tests/tmp_cutoff
+make.sh
+py_tests/sandbox/
+py_tests/src/config_simple_L.xyz
+py_tests/src/kernel.py
+py_tests/src/soap
+py_tests/src/test.py
+src/soap/tools/.ipynb_checkpoints/
+src/soap/tools/sandbox.ipynb
+test/configs/C60.xyz
+test/configs/C60_pair.xyz
+test/configs/DCV5T_ME3.xyz
+test/configs/d2t/
+test/configs/line.xyz
+test/configs/linedot.xyz
+test/configs/misc/
+test/density.load.gp
+test/l1.tab
+test/soap
+test/svd/
+test/test_integrals/d2t.tar
+test/test_integrals/system_alq3/
+test/test_integrals/system_dcv2t/
+test/test_integrals/system_dpbic/
+test/test_integrals/work_dcv2t/
+test/test_invert/soap
+test/test_invert/test_qnlm.py
+test/test_invert/vmdrender.py
+test/test_invert/vmdsetup.tcl
+test/test_invert/vmdtools.py
+test/test_invert_standalone/line.xyz
+test/test_invert_standalone/soap
+test/test_invert_standalone/vmdsetup.tcl
+test/test_kernelpot/ksize_1_xi_4
+test/test_kernelpot/ksize_2_xi_4
+test/test_kernelpot/load.gp
+test/test_kernelpot/load_3d.gp
+test/test_kernelpot/load_vec.gp
+test/test_kernelpot/log.xyz
+test/test_kernelpot/log_cg.xyz
+test/test_kernelpot/map_excludecenters_2_3_centerweight_0.0
+test/test_kernelpot/map_excludecenters_2_3_centerweight_0.0_no_2l+1
+test/test_kernelpot/map_excludecenters_2_3_centerweight_0.5
+test/test_kernelpot/map_excludecenters_2_3_centerweight_0.5_no_2l+1
+test/test_kernelpot/map_excludecenters_2_3_centerweight_0.5_with_2l+1
+test/test_kernelpot/map_excludecenters_2_3_centerweight_0.5_with_2l+1_vectors
+test/test_kernelpot/map_excludecenters_2_3_centerweight_1.0
+test/test_kernelpot/map_excludecenters_2_3_centerweight_1.0_no_2l+1
+test/test_kernelpot/map_excludecenters__centerweight_0.5_no_2l+1
+test/test_kernelpot/map_steep_conjgrad.py
+test/test_kernelpot/out
+test/test_kernelpot/out_global
+test/test_kernelpot/plot_global/
+test/test_kernelpot/plot_sanity_check/
+test/test_kernelpot/plot_sanity_check_summed/
+test/test_kernelpot/soap
+test/test_kernelpot/tmp
+test/test_kernelpot/tmp2
+test/test_multiprocessing/group_rnd_2048.tar
+test/test_multiprocessing/group_rnd_2048/
+test/test_multiprocessing/group_rnd_short/
+test/test_multiprocessing/process.py.fiddle
+test/test_multiprocessing/soap
+test/test_particle_collection/soap
+test/test_particle_collection/vmdsetup.tcl
+test/test_serialization/config_000057.xyz.spectrum.arch-2
+test/test_serialization/soap
+test/test_serialization/vmdsetup.tcl
+test/test_suite/
+test/test_types/soap
+test/tmp
+test/vmdsetup.tcl

cxx_tests/src/gtest_radialbasis.cpp

@@ -157,6 +157,51 @@ TEST_F(TestRadialBasisGaussian, computeCoefficientsGradients) {
     //std::cout << capture << std::endl;
 }
 
+/*
+TEST_F(TestRadialBasisGaussian, computeCoefficientsGradientsStdout) {
+
+    // PARAMETERS: SETUP
+    double sigma = 0.5;
+    soap::vec d(0.,1.,0.);
+    double dr = 0.05;
+    double N_r_samples = 100;    
+    std::vector< std::pair<int,int> > kl_list { 
+        std::pair<int,int>{0,0}, 
+        std::pair<int,int>{1,0}, 
+        std::pair<int,int>{2,0}, 
+        std::pair<int,int>{3,0}, 
+        std::pair<int,int>{4,0}, 
+        std::pair<int,int>{5,0}, 
+        std::pair<int,int>{6,0}, 
+        std::pair<int,int>{7,0}, 
+        std::pair<int,int>{8,0} };
+    
+    // OUTPUT: SETUP
+    int N = _radbasis->N();
+    int L = _options.get<int>("angularbasis.L");
+
+    soap::RadialBasis::radcoeff_t Gnl = soap::RadialBasis::radcoeff_zero_t(N,L+1);
+    soap::RadialBasis::radcoeff_t dGnl_dx = soap::RadialBasis::radcoeff_zero_t(N,L+1);
+    soap::RadialBasis::radcoeff_t dGnl_dy = soap::RadialBasis::radcoeff_zero_t(N,L+1);
+    soap::RadialBasis::radcoeff_t dGnl_dz = soap::RadialBasis::radcoeff_zero_t(N,L+1);
+    
+    // GENERATE
+    for (int i = 0; i < N_r_samples; ++i) {
+        double ri = i*dr;
+        _radbasis->computeCoefficients(d, ri, sigma, Gnl, &dGnl_dx, &dGnl_dy, &dGnl_dz);        
+        std::cout << boost::format("%1$+1.7f ") % ri << std::flush;
+        
+        for (auto kl = kl_list.begin(); kl != kl_list.end(); ++kl) {
+            int k = (*kl).first;
+            int l = (*kl).second;
+            std::cout << boost::format("%1$+1.7e ") %
+                Gnl(k,l) << std::flush;
+        }
+        std::cout << std::endl;
+    }
+}
+*/
+
 TEST_F(TestRadialBasisGaussian, NumericalIntegrationBessel) {
 
     // CHECK NUMERICAL INTEGRATION

test/test.py

@@ -22,7 +22,7 @@ element_mass = {
 ase_config_list = soap.tools.ase_load_all('configs')
 for config in ase_config_list:
     print config.config_file
-config = ase_config_list[1]
+config = ase_config_list[4]
 osio << config.atoms << endl
 
 sigma = 0.5
@@ -36,7 +36,7 @@ options.set('radialbasis.N', 9)
 options.set('radialbasis.sigma', sigma)
 options.set('radialbasis.integration_steps', 15)
 #options.set('radialbasis.N', 9)
-options.set('radialcutoff.Rc', 6.8)
+options.set('radialcutoff.Rc', 3.41)
 options.set('radialcutoff.Rc_width', 0.5)
 options.set('radialcutoff.type', 'shifted-cosine')
 options.set('radialcutoff.center_weight', 1.)
@@ -66,8 +66,8 @@ for atom in structure:
 spectrum = soap.Spectrum(structure, options)
 spectrum.compute()
 spectrum.computePower()
-spectrum.save("test_serialization/%s.spectrum.arch" % structure.label)
-spectrum.save("test_invert/%s.spectrum.arch" % structure.label)
+#spectrum.save("test_serialization/%s.spectrum.arch" % structure.label)
+#spectrum.save("test_invert/%s.spectrum.arch" % structure.label)
 
 spectrum.writeDensity(1, "C", "")
 spectrum.writePowerDensity(1, "C", "", "")