Merge pull request #215 from electronic-structure/develop

Develop
electronic-structure · May 18, 2018 · 535c252 · 535c252
2 parents 94931d5 + 311d5c2
commit 535c252
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Showing 15 changed files with 73 additions and 133 deletions.
diff --git a/apps/atoms/atom.cpp b/apps/atoms/atom.cpp
@@ -68,7 +68,7 @@ class Free_atom: public sirius::Atom_type
                 vrho[i] = 0;
             }
 
-            sirius::Mixer<double>* mixer = new sirius::Broyden1<double>(0, np, 12, 0.8, mpi_comm_self());
+            sirius::Mixer<double>* mixer = new sirius::Broyden1<double>(0, np, 12, 0.8, Communicator::self());
             for (int i = 0; i < np; i++) {
                 mixer->input_local(i, vrho[i]);
             }
@@ -633,7 +633,7 @@ void generate_atom_file(Free_atom& a,
     sirius::Atom_symmetry_class atom_class(0, a);
     atom_class.set_spherical_potential(veff);
     atom_class.generate_radial_functions(relativity_t::none);
-    runtime::pstdout pout(mpi_comm_self());
+    runtime::pstdout pout(Communicator::self());
     atom_class.write_enu(pout);
     pout.flush();
 

diff --git a/configure.py b/configure.py
@@ -6,7 +6,7 @@
 
 packages = {
     "spg"  : {
-        "url"     : "https://github.com/atztogo/spglib/archive/v1.9.9.tar.gz",
+        "url"     : "https://github.com/atztogo/spglib/archive/v1.10.3.tar.gz",
         "options" : []
     },
     "fftw" : {
@@ -190,7 +190,6 @@ def main():
     # add magma include paths
     if 'MAGMA_ROOT' in platform:
         makeinc.write("CXX_OPT := $(CXX_OPT) -I%s/include\n"%platform['MAGMA_ROOT']);
-        makeinc.write("CXX_OPT := $(CXX_OPT) -I%s/control\n"%platform['MAGMA_ROOT']);
     # add elpa include path
     if 'ELPA_ROOT' in platform:
         makeinc.write("CXX_OPT := $(CXX_OPT) -I%s/elpa\n"%platform['ELPA_ROOT']);

diff --git a/src/Potential/poisson.hpp b/src/Potential/poisson.hpp
@@ -221,7 +221,7 @@ inline void Potential::poisson(Periodic_function<double> const& rho)
         /* add contribution from the pseudo-charge */
         poisson_add_pseudo_pw(qmt, qit, const_cast<double_complex*>(&rho.f_pw_local(0)));
 
-        if (check_pseudo_charge) {
+        if (ctx_.control().verification_ >= 2) {
             poisson_sum_G(ctx_.lmmax_rho(), &rho.f_pw_local(0), sbessel_mom_, qit);
 
             double d = 0.0;

diff --git a/src/SDDK/GPU/magma.hpp b/src/SDDK/GPU/magma.hpp
@@ -7,7 +7,7 @@
 #include <magma.h>
 #include <magma_z.h>
 #include <magma_d.h>
-#include <magma_threadsetting.h>
+#include <../control/magma_threadsetting.h>
 #include <cstring>
 
 namespace magma {

diff --git a/src/SDDK/timer.hpp b/src/SDDK/timer.hpp
@@ -61,14 +61,14 @@ class timer
     {
         return timer_values()[label__];
     }
-    
+
     /// Mapping between parent timer and child timers.
     /** This map is needed to build a call tree of timers with the information about "self" time
         and time spent in calling other timers. */
     static std::map<std::string, std::map<std::string, double>>& timer_values_ex()
     {
         /* the following map is stored:
-           
+
            parent_timer_label1  |--- child_timer_label1, time1a
                                 |--- child timer_label2, time2
                                 |--- child_timer_label3, time3
@@ -83,7 +83,7 @@ class timer
     }
 
   public:
-    
+
     /// Constructor.
     timer(std::string label__)
         : label_(label__)
@@ -94,7 +94,7 @@ class timer
         stack().push_back(label_);
         active_ = true;
     }
-    
+
     /// Destructor.
     ~timer()
     {
@@ -105,7 +105,7 @@ class timer
             stop();
         }
     }
-    
+
     /// Stop the timer and update the statistics.
     double stop()
     {
@@ -116,7 +116,7 @@ class timer
         /* remove this timer name from the list; now last element contains
            the name of the parent timer */
         stack().pop_back();
-        
+
         /* measure the time difference */
         auto t2    = std::chrono::high_resolution_clock::now();
         auto tdiff = std::chrono::duration_cast<std::chrono::duration<double>>(t2 - starting_time_);
@@ -315,4 +315,4 @@ class timer
 /* this is needed only to call timer::global_timer() at the beginning */
 static timer* global_timer_init__ = &timer::global_timer();
 
-#endif // __SDDK_INTERNAL_HPP__
+#endif
diff --git a/src/SDDK/wave_functions.hpp b/src/SDDK/wave_functions.hpp
@@ -19,7 +19,7 @@
 
 /** \file wave_functions.hpp
  *
- *  \brief Contains declaration and implementation of wave_functions class.
+ *  \brief Contains declaration and implementation of Wave_functions class.
  */
 
 #ifndef __WAVE_FUNCTIONS_HPP__

diff --git a/src/SDDK/wf_inner.hpp b/src/SDDK/wf_inner.hpp
@@ -57,7 +57,7 @@ inline void inner(device_t        pu__,
                   int             irow0__,
                   int             jcol0__)
 {
-    PROFILE("sddk::wave_functions::inner");
+    PROFILE("sddk::Wave_functions::inner");
 
     static_assert(std::is_same<T, double>::value || std::is_same<T, double_complex>::value, "wrong type");
 

diff --git a/src/SDDK/wf_trans.hpp b/src/SDDK/wf_trans.hpp
@@ -1,5 +1,9 @@
 /// Linear transformation of the wave-functions.
-/** The transformation matrix is expected in the CPU memory. */
+/** The transformation matrix is expected in the CPU memory. The following operation is performed:
+ *  \f[
+ *     \psi^{out}_{j} = \alpha \sum_{i} \psi^{in}_{i} Z_{ij} + \beta \psi^{out}_{j}
+ *  \f]
+ */
 template <typename T>
 inline void transform(device_t                     pu__,
                       int                          ispn__,
@@ -15,7 +19,7 @@ inline void transform(device_t                     pu__,
                       int                          j0__,
                       int                          n__)
 {
-    PROFILE("sddk::wave_functions::transform");
+    PROFILE("sddk::Wave_functions::transform");
 
     static_assert(std::is_same<T, double>::value || std::is_same<T, double_complex>::value, "wrong type");
 
@@ -140,7 +144,7 @@ inline void transform(device_t                     pu__,
         }
     };
 
-    sddk::timer t1("sddk::wave_functions::transform|init");
+    sddk::timer t1("sddk::Wave_functions::transform|init");
     /* initial values for the resulting wave-functions */
     for (int iv = 0; iv < nwf; iv++) {
         if (beta__ == 0) {
@@ -370,7 +374,6 @@ inline void transform(device_t        pu__,
                       int             j0__,
                       int             n__)
 {
-
     transform<T>(pu__, ispn__, alpha__, {&wf_in__}, i0__, m__, mtrx__, irow0__, jcol0__, beta__, {&wf_out__}, j0__, n__);
 }
 
@@ -387,75 +390,6 @@ inline void transform(device_t        pu__,
                       int             j0__,
                       int             n__)
 {
-
     transform<T>(pu__, ispn__, 1.0, {&wf_in__}, i0__, m__, mtrx__, irow0__, jcol0__, 0.0, {&wf_out__}, j0__, n__);
 }
 
-//== /// Linear transformation of wave-functions.
-//== /** The following operation is performed:
-//==  *  \f[
-//==  *     \psi^{out}_{j} = \alpha \sum_{i} \psi^{in}_{i} Z_{ij} + \beta \psi^{out}_{j}
-//==  *  \f]
-//==  */
-//== template <typename T>
-//== inline void transform(device_t pu__,
-//==                       double          alpha__,
-//==                       wave_functions& wf_in__,
-//==                       int             i0__,
-//==                       int             m__,
-//==                       dmatrix<T>&     mtrx__,
-//==                       int             irow0__,
-//==                       int             jcol0__,
-//==                       double          beta__,
-//==                       wave_functions& wf_out__,
-//==                       int             j0__,
-//==                       int             n__)
-//== {
-//==     transform<T>(pu__, alpha__, {&wf_in__}, i0__, m__, mtrx__, irow0__, jcol0__, beta__, {&wf_out__}, j0__, n__);
-//== }
-//==
-//== template <typename T>
-//== inline void transform(device_t        pu__,
-//==                       wave_functions& wf_in__,
-//==                       int             i0__,
-//==                       int             m__,
-//==                       dmatrix<T>&     mtrx__,
-//==                       int             irow0__,
-//==                       int             jcol0__,
-//==                       wave_functions& wf_out__,
-//==                       int             j0__,
-//==                       int             n__)
-//== {
-//==     transform<T>(pu__, 1.0, {&wf_in__}, i0__, m__, mtrx__, irow0__, jcol0__, 0.0, {&wf_out__}, j0__, n__);
-//== }
-//==
-//== template <typename T>
-//== inline void transform(device_t                     pu__,
-//==                       double                       alpha__,
-//==                       std::vector<Wave_functions*> wf_in__,
-//==                       int                          i0__,
-//==                       int                          m__,
-//==                       dmatrix<T>&                  mtrx__,
-//==                       int                          irow0__,
-//==                       int                          jcol0__,
-//==                       double                       beta__,
-//==                       std::vector<Wave_functions*> wf_out__,
-//==                       int                          j0__,
-//==                       int                          n__)
-//== {
-//==     assert(wf_in__.size() == wf_out__.size());
-//==     for (size_t i = 0; i < wf_in__.size(); i++) {
-//==         assert(wf_in__[i]->num_components() == wf_in__[0]->num_components());
-//==         assert(wf_in__[i]->num_components() == wf_out__[i]->num_components());
-//==     }
-//==     int num_sc = wf_in__[0]->num_components();
-//==     for (int is = 0; is < num_sc; is++) {
-//==         std::vector<wave_functions*> wf_in;
-//==         std::vector<wave_functions*> wf_out;
-//==         for (size_t i = 0; i < wf_in__.size(); i++) {
-//==             wf_in.push_back(&wf_in__[i]->component(is));
-//==             wf_out.push_back(&wf_out__[i]->component(is));
-//==         }
-//==         transform(pu__, alpha__, wf_in, i0__, m__, mtrx__, irow0__, jcol0__, beta__, wf_out, j0__, n__);
-//==     }
-//== }
diff --git a/src/Unit_cell/free_atom.hpp b/src/Unit_cell/free_atom.hpp
@@ -38,7 +38,7 @@ class Free_atom : public Atom_type
     /// Radial wave-functions.
     mdarray<double, 2> free_atom_wave_functions_;
     /// Atomic potential.
-    Spline<double> free_atom_potential_;
+    Spline<double> free_atom_potential_; // TODO: rename. this is potential of electronic density
     /// NIST total energy for LDA calculation.
     double NIST_LDA_Etot_{0};
     /// NIST total energy for scalar-relativistic LDA calculation.
@@ -211,7 +211,7 @@ class Free_atom : public Atom_type
             }
 
             for (int i = 0; i < np; i++) {
-                f(i) = (veff[i] - vnuc[i]) * rho(i);
+                f(i) = vrho[i] * rho(i);
             }
             /* kinetic energy */
             energy_kin = eval_sum - fourpi * (f.interpolate().integrate(2) - zn() * rho.integrate(1));
@@ -329,6 +329,11 @@ class Free_atom : public Atom_type
     {
         return free_atom_potential_.at_point(x);
     }
+
+    inline Spline<double>& free_atom_potential()
+    {
+        return free_atom_potential_;
+    }
 };
 } // namespace sirius
 

diff --git a/src/Unit_cell/unit_cell_symmetry.h b/src/Unit_cell/unit_cell_symmetry.h
@@ -26,7 +26,11 @@
 #define __UNIT_CELL_SYMMETRY_H__
 
 extern "C" {
+#ifdef __SPGLIB_STD_INCLUDE_PATH
+#include <spglib/spglib.h>
+#else
 #include <spglib.h>
+#endif
 }
 
 #include "geometry3d.hpp"

diff --git a/src/config.h b/src/config.h
@@ -73,10 +73,7 @@ const bool test_spinor_wf = false;
 
 const bool hdf5_trace_errors = false;
 
-/// True if pseudocharge moments in LAPW Poisson solver have to be checked and compared with true multipole moments.
-const bool check_pseudo_charge = false;
-
-/// Tru if LAPW Hamiltonian is diagonalized with second-variational approach.
+/// True if LAPW Hamiltonian is diagonalized with second-variational approach.
 const bool use_second_variation = true;
 
 /// True if wave-functions are permanently kept on a GPU and not allocated/deallocated.

diff --git a/src/dft_ground_state.h b/src/dft_ground_state.h
@@ -940,7 +940,7 @@ inline void DFT_ground_state::print_magnetic_moment()
 
 #endif // __DFT_GROUND_STATE_H__
 
-/** \page DFT Spin-polarized DFT
+/** \page dft Spin-polarized DFT
  *  \section section1 Preliminary notes
  *
  *  \note Here and below sybol \f$ {\boldsymbol \sigma} \f$ is reserved for the vector of Pauli matrices. Spin components

diff --git a/src/matching_coefficients.h b/src/matching_coefficients.h
@@ -88,7 +88,7 @@ class Matching_coefficients
             /* invert matrix of radial derivatives */
             switch (N) {
                 case 1: {
-                    if (unit_cell_.parameters().control().verification_ > 0) {
+                    if (unit_cell_.parameters().control().verification_ >= 1) {
                         if (std::abs(A(0, 0)) < 1.0 / std::sqrt(unit_cell_.omega())) {   
                             std::stringstream s;
                             s << "Ill defined plane wave matching problem for atom type " << iat << ", l = " << l << std::endl
@@ -103,7 +103,7 @@ class Matching_coefficients
                 case 2: {
                     double det = A(0, 0) * A(1, 1) - A(0, 1) * A(1, 0);
 
-                    if (unit_cell_.parameters().control().verification_ > 0) {
+                    if (unit_cell_.parameters().control().verification_ >= 1) {
                         if (std::abs(det) < 1.0 / std::sqrt(unit_cell_.omega())) {   
                             std::stringstream s;
                             s << "Ill defined plane wave matching problem for atom type " << iat << ", l = " << l << std::endl

diff --git a/src/sbessel.h b/src/sbessel.h
@@ -22,8 +22,8 @@
  *  \brief Contains implementation of sirius::Spherical_Bessel_functions and sirius::sbessel_approx classes.
  */
 
-#ifndef __SBESSEL_PW_H__
-#define __SBESSEL_PW_H__
+#ifndef __SBESSEL_H__
+#define __SBESSEL_H__
 
 #include <gsl/gsl_sf_bessel.h>
 #include "eigenproblem.h"