From e436e176b229d0a21f001771c7e702b7f90f2b10 Mon Sep 17 00:00:00 2001
From: mkirsz <s1351949@sms.ed.ac.uk>
Date: Mon, 24 Feb 2025 11:13:15 +0000
Subject: [PATCH] wip
---
.../tadah/mlip/design_matrix/design_matrix.h | 14 ++-
.../functions/basis_functions/dm_bf_linear.h | 6 +-
.../basis_functions/dm_bf_polynomial2.h | 6 +-
.../functions/dm_function_base.h | 7 +-
.../functions/kernels/dm_kern_base.h | 7 +-
.../functions/kernels/dm_kern_linear.h | 6 +-
include/tadah/mlip/neighbor_list_db.h | 14 +--
include/tadah/mlip/structure.h | 14 +++
include/tadah/mlip/structure_neighbor_view.h | 109 ++++++++++++++++--
src/dm_bf_linear.cpp | 6 +-
src/dm_bf_polynomial2.cpp | 35 ++++--
src/dm_kern_base.cpp | 6 +-
src/dm_kern_linear.cpp | 6 +-
13 files changed, 179 insertions(+), 57 deletions(-)
diff --git a/include/tadah/mlip/design_matrix/design_matrix.h b/include/tadah/mlip/design_matrix/design_matrix.h
index 168b94b..a19ba9b 100644
--- a/include/tadah/mlip/design_matrix/design_matrix.h
+++ b/include/tadah/mlip/design_matrix/design_matrix.h
@@ -1,6 +1,7 @@
#ifndef DESIGN_MATRIX_H
#define DESIGN_MATRIX_H
+#include "tadah/mlip/structure_neighbor_view.h"
#include <tadah/mlip/st_descriptors_db.h>
#include <tadah/mlip/structure_db.h>
#include <tadah/mlip/descriptors_calc.h>
@@ -11,6 +12,7 @@
#include <tadah/mlip/memory/DesignMatrixWorkspace.h>
#include <tadah/mlip/neighbor_list_db.h>
+#include <tadah/mlip/structure_neighbor_view.h>
#include <stdexcept>
@@ -202,30 +204,32 @@ public:
#endif
for (size_t s=0; s<stdb.size(); ++s) {
StDescriptors st_d = dc.calc(stdb(s), nldb);
+ // StructureNeighborView st_nb(nldb,s); // but we need to know the structure offset in global arrays
+ StructureNeighborView st_nb(nldb.nlist(),stdb(s));
if(config.get<bool>("NORM"))
norm.normalise(st_d);
- build(rows[s], stdb(s), nldb, st_d);
+ build(rows[s], stdb(s), nldb, st_nb, st_d);
}
}
- void build(size_t &row, const Structure &st, const StDescriptors &st_d) {
+ void build(size_t &row, const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d) {
double escale = 1;
if (scale) escale = st.eweight*eweightglob/st.natoms();
- f.calc_phi_energy_row(ws->Phi,row,escale,st,st_d);
+ f.calc_phi_energy_row(ws->Phi,row,escale,st,st_nb,st_d);
if (force) {
double fscale = 1;
if (scale) fscale = st.fweight*fweightglob/st.natoms()/3.0;///f_std_dev;
- f.calc_phi_force_rows(ws->Phi,row,fscale,st,st_d);
+ f.calc_phi_force_rows(ws->Phi,row,fscale,st,st_nb,st_d);
}
if (stress) {
double sscale_arr[6] {1,1,1,1,1,1};
if (scale)
for(size_t xy=0;xy<6;++xy)
sscale_arr[xy] = st.sweight*sweightglob/6.0;///s_std_dev[xy];
- f.calc_phi_stress_rows(ws->Phi,row,sscale_arr,st,st_d);
+ f.calc_phi_stress_rows(ws->Phi,row,sscale_arr,st,st_nb,st_d);
}
}
void fill_T(const StructureDB &stdb, size_t start=0) {
diff --git a/include/tadah/mlip/design_matrix/functions/basis_functions/dm_bf_linear.h b/include/tadah/mlip/design_matrix/functions/basis_functions/dm_bf_linear.h
index 6fa887d..96312bf 100644
--- a/include/tadah/mlip/design_matrix/functions/basis_functions/dm_bf_linear.h
+++ b/include/tadah/mlip/design_matrix/functions/basis_functions/dm_bf_linear.h
@@ -12,11 +12,11 @@ struct DM_BF_Linear: public DM_BF_Base, public BF_Linear
DM_BF_Linear(const Config &c);
size_t get_phi_cols(const Config &config) override;
void calc_phi_energy_row(phi_type &Phi, size_t &row,
- const double fac, const Structure &st, const StDescriptors &st_d) override;
+ const double fac, const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d) override;
void calc_phi_force_rows(phi_type &Phi, size_t &row,
- const double fac, const Structure &st, const StDescriptors &st_d) override;
+ const double fac, const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d) override;
void calc_phi_stress_rows(phi_type &Phi, size_t &row,
- const double fac[6], const Structure &st, const StDescriptors &st_d) override;
+ const double fac[6], const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d) override;
};
}
}
diff --git a/include/tadah/mlip/design_matrix/functions/basis_functions/dm_bf_polynomial2.h b/include/tadah/mlip/design_matrix/functions/basis_functions/dm_bf_polynomial2.h
index bda5f5a..7bc796e 100644
--- a/include/tadah/mlip/design_matrix/functions/basis_functions/dm_bf_polynomial2.h
+++ b/include/tadah/mlip/design_matrix/functions/basis_functions/dm_bf_polynomial2.h
@@ -12,11 +12,11 @@ struct DM_BF_Polynomial2: public DM_BF_Base, public BF_Polynomial2
DM_BF_Polynomial2(const Config &c);
size_t get_phi_cols(const Config &config) override;
void calc_phi_energy_row(phi_type &Phi, size_t &row,
- const double fac, const Structure &st, const StDescriptors &st_d) override;
+ const double fac, const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d) override;
void calc_phi_force_rows(phi_type &Phi, size_t &row,
- const double fac, const Structure &st, const StDescriptors &st_d) override;
+ const double fac, const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d) override;
void calc_phi_stress_rows(phi_type &Phi, size_t &row,
- const double fac[6], const Structure &st, const StDescriptors &st_d) override;
+ const double fac[6], const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d) override;
};
}
}
diff --git a/include/tadah/mlip/design_matrix/functions/dm_function_base.h b/include/tadah/mlip/design_matrix/functions/dm_function_base.h
index 49e92bc..8d40e9f 100644
--- a/include/tadah/mlip/design_matrix/functions/dm_function_base.h
+++ b/include/tadah/mlip/design_matrix/functions/dm_function_base.h
@@ -7,6 +7,7 @@
#include <tadah/models/functions/function_base.h>
#include <tadah/mlip/structure.h>
#include <tadah/mlip/st_descriptors.h>
+#include <tadah/mlip/structure_neighbor_view.h>
#include <iomanip>
#include <iostream>
@@ -25,11 +26,11 @@ struct DM_Function_Base: public virtual Function_Base {
virtual size_t get_phi_cols(const Config &)=0;
virtual void calc_phi_energy_row(phi_type &, size_t &,
- const double , const Structure &, const StDescriptors &)=0;
+ const double , const Structure &, const StructureNeighborView &st_nb, const StDescriptors &)=0;
virtual void calc_phi_force_rows(phi_type &, size_t &,
- const double , const Structure &, const StDescriptors &)=0;
+ const double , const Structure &, const StructureNeighborView &st_nb, const StDescriptors &)=0;
virtual void calc_phi_stress_rows(phi_type &, size_t &,
- const double[6], const Structure &, const StDescriptors &)=0;
+ const double[6], const Structure &, const StructureNeighborView &st_nb, const StDescriptors &)=0;
};
}
}
diff --git a/include/tadah/mlip/design_matrix/functions/kernels/dm_kern_base.h b/include/tadah/mlip/design_matrix/functions/kernels/dm_kern_base.h
index 5bc532c..996dce6 100644
--- a/include/tadah/mlip/design_matrix/functions/kernels/dm_kern_base.h
+++ b/include/tadah/mlip/design_matrix/functions/kernels/dm_kern_base.h
@@ -7,6 +7,7 @@
#include <tadah/mlip/st_descriptors.h>
#include <tadah/core/core_types.h>
#include <tadah/models/functions/kernels/kern_base.h>
+#include <tadah/mlip/structure_neighbor_view.h>
#include <iostream>
namespace tadah {
@@ -26,9 +27,9 @@ class DM_Kern_Base: public DM_Function_Base, public virtual Kern_Base {
DM_Kern_Base(const Config&c);
virtual ~DM_Kern_Base();
virtual size_t get_phi_cols(const Config &config) override;
- virtual void calc_phi_energy_row(phi_type &Phi, size_t &row, const double fac, const Structure &st, const StDescriptors &st_d) override;
- virtual void calc_phi_force_rows(phi_type &Phi, size_t &row, const double fac, const Structure &st, const StDescriptors &st_d) override;
- virtual void calc_phi_stress_rows(phi_type &Phi, size_t &row, const double fac[6], const Structure &st, const StDescriptors &st_d) override;
+ virtual void calc_phi_energy_row(phi_type &Phi, size_t &row, const double fac, const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d) override;
+ virtual void calc_phi_force_rows(phi_type &Phi, size_t &row, const double fac, const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d) override;
+ virtual void calc_phi_stress_rows(phi_type &Phi, size_t &row, const double fac[6], const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d) override;
};
}
diff --git a/include/tadah/mlip/design_matrix/functions/kernels/dm_kern_linear.h b/include/tadah/mlip/design_matrix/functions/kernels/dm_kern_linear.h
index fcad6b9..968478d 100644
--- a/include/tadah/mlip/design_matrix/functions/kernels/dm_kern_linear.h
+++ b/include/tadah/mlip/design_matrix/functions/kernels/dm_kern_linear.h
@@ -23,11 +23,11 @@ class DM_Kern_Linear : public DM_Kern_Base, public Kern_Linear {
size_t get_phi_cols(const Config &config) override;
void calc_phi_energy_row(phi_type &Phi, size_t &row,
- const double fac, const Structure &st, const StDescriptors &st_d) override;
+ const double fac, const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d) override;
void calc_phi_force_rows(phi_type &Phi, size_t &row,
- const double fac, const Structure &st, const StDescriptors &st_d) override;
+ const double fac, const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d) override;
void calc_phi_stress_rows(phi_type &Phi, size_t &row,
- const double fac[6], const Structure &st, const StDescriptors &st_d) override;
+ const double fac[6], const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d) override;
};
}
}
diff --git a/include/tadah/mlip/neighbor_list_db.h b/include/tadah/mlip/neighbor_list_db.h
index f716070..acd4ea4 100644
--- a/include/tadah/mlip/neighbor_list_db.h
+++ b/include/tadah/mlip/neighbor_list_db.h
@@ -5,7 +5,7 @@
#include <tadah/mlip/neighbor_list.h>
#include <tadah/mlip/structure_db.h>
-#include <tadah/mlip/structure_neighbor_view.h>
+// #include <tadah/mlip/structure_neighbor_view.h>
namespace tadah {
namespace mlip {
@@ -58,7 +58,7 @@ public:
if (localAtomIndex >= sRef.natoms()) {
throw std::out_of_range("NeighborListDB::toGlobalAtomIndex: localAtomIndex out of range");
}
- return sRef.offset_ + localAtomIndex;
+ return sRef.offset() + localAtomIndex;
}
/**
@@ -112,11 +112,11 @@ public:
* @param s A reference to the chosen Structure from the same DB.
* @return A lightweight view object referencing the HPC data subrange for s.
*/
- inline StructureNeighborView createStructureView(const Structure &s) const
- {
- // Optionally check that s.db_ == &db_ if you want to ensure they belong together.
- return StructureNeighborView(nlist_, s);
- }
+ // inline StructureNeighborView createStructureView(const Structure &s) const
+ // {
+ // // Optionally check that s.db_ == &db_ if you want to ensure they belong together.
+ // return StructureNeighborView(nlist_, s);
+ // }
private:
/**
diff --git a/include/tadah/mlip/structure.h b/include/tadah/mlip/structure.h
index f0c6653..5bafff0 100644
--- a/include/tadah/mlip/structure.h
+++ b/include/tadah/mlip/structure.h
@@ -87,6 +87,20 @@ public:
Vec3dSoAView positionView(size_t i);
Vec3dSoAView forceView(size_t i);
+ /**
+ * @brief Converts a global index to a local index within this structure.
+ *
+ */
+inline std::size_t globalToLocal(std::size_t gIdx) const {
+ // Check if gIdx belongs to this structure’s subrange
+ if (gIdx < offset_ || gIdx >= (offset_ + size_)) {
+ throw std::runtime_error(
+ "globalToLocal: global index not in this structure's subrange"
+ );
+ }
+ return gIdx - offset_;
+}
+
// --------------------------------------------------
// Minimal I/O
// --------------------------------------------------
diff --git a/include/tadah/mlip/structure_neighbor_view.h b/include/tadah/mlip/structure_neighbor_view.h
index 277f317..21b9b1b 100644
--- a/include/tadah/mlip/structure_neighbor_view.h
+++ b/include/tadah/mlip/structure_neighbor_view.h
@@ -2,10 +2,10 @@
#include <cstddef>
#include <stdexcept>
-#include "neighbor_list.h"
-#include "structure_db.h"
-#include "structure.h"
-#include "neighbor_list_db.h"
+#include <tadah/mlip/neighbor_list.h>
+#include <tadah/mlip/structure_db.h>
+#include <tadah/mlip/structure.h>
+#include <tadah/mlip/neighbor_list_db.h>
namespace tadah {
namespace mlip {
@@ -35,16 +35,17 @@ public:
}
/**
- * @brief Constructs by picking a structure from NeighborListDB.db()(structureIndex),
- * then referencing the HPC neighbor list from nlDB.nlist().
+ * @brief Constructs by picking a structure from StructureDB(structureIndex),
+ * then referencing the HPC neighbor list from nldb.nlist().
*
* This avoids manually retrieving the Structure from StructureDB first.
*
- * @param nlDB The neighbor-list DB that references a single HPC neighbor list & DB.
- * @param structureIndex The index of the desired structure in nlDB.db().
+ * @param stdb StructureDB containing the desired structure.
+ * @param nldb The neighbor-list DB that references a single HPC neighbor list & stdb.
+ * @param structureIndex The index of the desired structure in stdb.
*/
- StructureNeighborView(const NeighborListDB &nlDB, std::size_t structureIndex)
- : globalList_(nlDB.nlist()), str_(nlDB.db()(structureIndex))
+ StructureNeighborView(const StructureDB &stdb, const NeighborListDB &nldb, std::size_t structureIndex)
+ : globalList_(nldb.nlist()), str_(stdb(structureIndex))
{
// Minimal checks can be added if needed.
}
@@ -115,5 +116,91 @@ public:
* @brief Returns the Z-shift pointer.
*/
inline const int* getShiftZPtr(std::size_t localAtomIndex) const {
- if (localAtomIndex >= str_.nat
+ if (localAtomIndex >= str_.natoms()) {
+ throw std::out_of_range("StructureNeighborView::getShiftZPtr: local index out of range");
+ }
+ std::size_t gIdx = str_.offset() + localAtomIndex;
+ return globalList_.getShiftZPtr(gIdx);
+ }
+
+private:
+ /**
+ * @brief Reference to the single global HPC neighbor list (covering all atoms).
+ */
+ const NeighborList &globalList_;
+
+ /**
+ * @brief The targeted structure from the HPC DB, which provides offset() and natoms().
+ */
+ const Structure &str_;
+
+ /**
+ * @brief Returns the local index (ii) of the i-th atom within the j-th atom's neighbor list.
+ *
+ * This method uses mirror information stored in the neighbor list to identify
+ * the "reverse" index in the j-th atom's neighbor list that corresponds to
+ * the i-th atom. The parameter jj must be the position of j in i's neighbor list.
+ * i and j are local indices within the current structure (not global HPC indices).
+ *
+ * Basic checks:
+ * - 0 <= i < numAtoms()
+ * - 0 <= j < numAtoms()
+ * - 0 <= jj < numNeighbors(i)
+ *
+ * The logic:
+ * 1. Global HPC indices (gi, gj) are computed by adding each local index (i, j) to the structure offset.
+ * 2. mirrorOffset is fetched from the global neighbor list using getMirrorOffset(gi, jj).
+ * This mirrorOffset indicates the flattened position in j's neighbor entries pointing back to i.
+ * 3. prefixSum_[gj] is the start offset of j's neighbors in the flattened global array.
+ * 4. Subtracting prefixSum_[gj] from mirrorOffset gives the local index of i in j's neighbor list (ii).
+ *
+ * Example usage within HPC pairwise iteration:
+ * - One loops over each atom i in the structure.
+ * - Then over each neighbor index jj of i (pointing to neighbor j).
+ * - getAAIndex(i, j, jj) yields the local index ii (where i is found in j's neighbor list).
+ * - This ensures consistent symmetrical housekeeping in pair computations.
+ *
+ * @param i Local index of the first atom.
+ * @param j Local index of the second atom (neighbor).
+ * @param jj Position of j in i's neighbor list.
+ * @return The local index (ii) of i in j's neighbor list.
+ */
+ inline size_t getAAIndex(const size_t i, const size_t j, const size_t jj)
+ {
+ // Verify bounds on i, j, and jj to avoid out-of-range errors.
+ // i, j, and jj must be valid for this structure.
+ if (i >= str_.natoms() || j >= str_.natoms()) {
+ throw std::out_of_range("StructureNeighborView::getAAIndex: atom index out of range");
+ }
+ if (jj >= globalList_.numNeighbors(str_.offset() + i)) {
+ throw std::out_of_range("StructureNeighborView::getAAIndex: neighbor index out of range");
+ }
+
+ // Convert local indices (i, j) to global HPC indices (gi, gj).
+ const size_t gi = str_.offset() + i;
+ const size_t gj = str_.offset() + j;
+
+ // Retrieve the flattened mirror offset for i <-> j.
+ // This offset indicates the actual position in j's neighbor array pointing back to i.
+ const size_t mirrorOffset = globalList_.getMirrorOffset(gi, jj);
+
+ // Identify j's subarray start in the flattened array.
+ // prefixData()[gj] is the offset in the neighbors array for atom gj.
+ const size_t jPrefix = globalList_.prefixData()[gj];
+
+ // The difference between mirrorOffset and j's prefix offset
+ // yields the local index of i in j's neighbor list.
+ const size_t ii = mirrorOffset - jPrefix;
+
+ // Optional check: ensure ii is within valid neighbor range for j.
+ if (ii >= globalList_.numNeighbors(gj)) {
+ throw std::out_of_range("StructureNeighborView::getAAIndex: computed mirror index out of range");
+ }
+
+ return ii;
+ }
+};
+
+} // namespace mlip
+} // namespace tadah
diff --git a/src/dm_bf_linear.cpp b/src/dm_bf_linear.cpp
index 7d576fa..483c263 100644
--- a/src/dm_bf_linear.cpp
+++ b/src/dm_bf_linear.cpp
@@ -17,7 +17,7 @@ size_t DM_BF_Linear::get_phi_cols(const Config &config)
return cols;
}
void DM_BF_Linear::calc_phi_energy_row(phi_type &Phi, size_t &row,
- const double fac, const Structure &, const StDescriptors &st_d)
+ const double fac, const Structure &, const StructureNeighborView &st_nb, const StDescriptors &st_d)
{
for (size_t i=0; i<st_d.naed(); ++i) {
const aed_type &aed = st_d.get_aed(i);
@@ -28,7 +28,7 @@ void DM_BF_Linear::calc_phi_energy_row(phi_type &Phi, size_t &row,
row++;
}
void DM_BF_Linear::calc_phi_force_rows(phi_type &Phi, size_t &row,
- const double fac, const Structure &st, const StDescriptors &st_d)
+ const double fac, const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d)
{
for (size_t a=0; a<st.natoms(); ++a) {
@@ -47,7 +47,7 @@ void DM_BF_Linear::calc_phi_force_rows(phi_type &Phi, size_t &row,
}
}
void DM_BF_Linear::calc_phi_stress_rows(phi_type &Phi, size_t &row,
- const double fac[6], const Structure &st, const StDescriptors &st_d)
+ const double fac[6], const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d)
{
double V_inv = 1/st.get_volume();
for (size_t i=0; i<st.natoms(); ++i) {
diff --git a/src/dm_bf_polynomial2.cpp b/src/dm_bf_polynomial2.cpp
index ddc417e..24f22e3 100644
--- a/src/dm_bf_polynomial2.cpp
+++ b/src/dm_bf_polynomial2.cpp
@@ -21,7 +21,7 @@ size_t DM_BF_Polynomial2::get_phi_cols(const Config &config)
void DM_BF_Polynomial2::calc_phi_energy_row(phi_type &Phi,
size_t &row,
const double fac,
- const Structure &,
+ const Structure &, const StructureNeighborView &st_nb,
const StDescriptors &st_d)
{
for (size_t a=0; a<st_d.naed();++a) {
@@ -38,14 +38,22 @@ void DM_BF_Polynomial2::calc_phi_energy_row(phi_type &Phi,
void DM_BF_Polynomial2::calc_phi_force_rows(phi_type &Phi,
size_t &row,
const double fac,
- const Structure &st,
+ const Structure &st, const StructureNeighborView &st_nb,
const StDescriptors &st_d)
{
for (size_t a=0; a<st.natoms(); ++a) {
+
+ const std::size_t* NbPtr = st_nb.getNeighborsPtr(a);
+ size_t NNbrs = st_nb.numNeighbors(a);
+ const Vec3dSoAView ri = st.positionView(a);
const aed_type& aedi = st_d.get_aed(a);
- for (size_t jj=0; jj<st_d.fd[a].size(); ++jj) {
- const size_t j=st.near_neigh_idx[a][jj];
- size_t aa = st.get_nn_iindex(a,j,jj);
+
+ for (size_t jj=0; jj<NNbrs; ++jj) {
+
+ size_t gj = NbPtr[jj];
+ size_t j= st.globalToLocal(gj); // j is local to st
+ size_t aa = getAAIndex(a, j, jj)
+ const aed_type& aedi = st_d.get_aed(a);
const fd_type &fdji = st_d.fd[j][aa];
const fd_type &fdij = st_d.fd[a][jj];
const aed_type& aedj = st_d.get_aed(j);
@@ -68,16 +76,22 @@ void DM_BF_Polynomial2::calc_phi_force_rows(phi_type &Phi,
void DM_BF_Polynomial2::calc_phi_stress_rows(phi_type &Phi,
size_t &row,
const double fac[6],
- const Structure &st,
+ const Structure &st, const StructureNeighborView &st_nb,
const StDescriptors &st_d)
{
double V_inv = 1/st.get_volume();
for (size_t a=0; a<st.natoms(); ++a) {
- const Vec3d &ri = st(a).position;
+
+ const std::size_t* NbPtr = st_nb.getNeighborsPtr(a);
+ size_t NNbrs = st_nb.numNeighbors(a);
+ const Vec3dSoAView ri = st.positionView(a);
const aed_type& aedi = st_d.get_aed(a);
- for (size_t jj=0; jj<st_d.fd[a].size(); ++jj) {
- const size_t j=st.near_neigh_idx[a][jj];
- size_t aa = st.get_nn_iindex(a,j,jj);
+
+ for (size_t jj=0; jj<NNbrs; ++jj) {
+
+ size_t gj = NbPtr[jj];
+ size_t j= st.globalToLocal(gj); // j is local to st
+ size_t aa = getAAIndex(a, j, jj)
const fd_type &fdji = st_d.fd[j][aa];
const fd_type &fdij = st_d.fd[a][jj];
const Vec3d &rj = st.nn_pos(a,jj);
@@ -101,5 +115,6 @@ void DM_BF_Polynomial2::calc_phi_stress_rows(phi_type &Phi,
}
row += 6;
}
+
}
}
diff --git a/src/dm_kern_base.cpp b/src/dm_kern_base.cpp
index f3fe327..28df869 100644
--- a/src/dm_kern_base.cpp
+++ b/src/dm_kern_base.cpp
@@ -16,7 +16,7 @@ size_t DM_Kern_Base::get_phi_cols(const Config &)
return basis.cols();
}
void DM_Kern_Base::calc_phi_energy_row(phi_type &Phi, size_t &row, const double fac,
- const Structure &, const StDescriptors &st_d)
+ const Structure &, const StructureNeighborView &st_nb, const StDescriptors &st_d)
{
for (size_t a=0; a<st_d.naed();++a) {
for (size_t b=0; b<basis.cols(); ++b) {
@@ -27,7 +27,7 @@ void DM_Kern_Base::calc_phi_energy_row(phi_type &Phi, size_t &row, const double
//Phi.row(row++) *= fac;
}
void DM_Kern_Base::calc_phi_force_rows(phi_type &Phi, size_t &row, const double fac,
- const Structure &st, const StDescriptors &st_d) {
+ const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d) {
for (size_t i=0; i<st.natoms(); ++i) {
const aed_type& aedi = st_d.get_aed(i);
for (size_t jj=0; jj<st_d.fd[i].size(); ++jj) {
@@ -47,7 +47,7 @@ void DM_Kern_Base::calc_phi_force_rows(phi_type &Phi, size_t &row, const double
}
}
void DM_Kern_Base::calc_phi_stress_rows(phi_type &Phi, size_t &row, const double fac[6],
- const Structure &st, const StDescriptors &st_d)
+ const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d)
{
double V_inv = 1/st.get_volume();
for (size_t i=0; i<st.natoms(); ++i) {
diff --git a/src/dm_kern_linear.cpp b/src/dm_kern_linear.cpp
index dc12670..dc5a898 100644
--- a/src/dm_kern_linear.cpp
+++ b/src/dm_kern_linear.cpp
@@ -18,7 +18,7 @@ size_t DM_Kern_Linear::get_phi_cols(const Config &config)
return cols;
}
void DM_Kern_Linear::calc_phi_energy_row(phi_type &Phi, size_t &row,
- const double fac, const Structure &, const StDescriptors &st_d)
+ const double fac, const Structure &, const StructureNeighborView &st_nb, const StDescriptors &st_d)
{
for (size_t a=0; a<st_d.naed();++a) {
const aed_type &aed = st_d.get_aed(a); // TODO
@@ -29,7 +29,7 @@ void DM_Kern_Linear::calc_phi_energy_row(phi_type &Phi, size_t &row,
row++;
}
void DM_Kern_Linear::calc_phi_force_rows(phi_type &Phi, size_t &row,
- const double fac, const Structure &st, const StDescriptors &st_d)
+ const double fac, const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d)
{
for (size_t a=0; a<st.natoms(); ++a) {
for (size_t jj=0; jj<st_d.fd[a].size(); ++jj) {
@@ -48,7 +48,7 @@ void DM_Kern_Linear::calc_phi_force_rows(phi_type &Phi, size_t &row,
}
void DM_Kern_Linear::calc_phi_stress_rows(phi_type &Phi, size_t &row,
- const double fac[6], const Structure &st, const StDescriptors &st_d)
+ const double fac[6], const Structure &st, const StructureNeighborView &st_nb, const StDescriptors &st_d)
{
double V_inv = 1/st.get_volume();
for (size_t i=0; i<st.natoms(); ++i) {
--
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