replace PaddedRVecVector by gmx::HostVector<gmx::RVec>

src/gromacs/fda/DistributedForces.cpp

@@ -90,7 +90,7 @@ void DistributedForces::write_detailed_vector(std::ostream& os) const
     }
 }
 
-void DistributedForces::write_detailed_scalar(std::ostream& os, PaddedRVecVector const& x) const
+void DistributedForces::write_detailed_scalar(std::ostream& os, gmx::HostVector<gmx::RVec> const& x) const
 {
     for (size_t i = 0; i != detailed.size(); ++i) {
         auto const& detailed_i = detailed[i];
@@ -125,7 +125,7 @@ void DistributedForces::write_summed_vector(std::ostream& os) const
     }
 }
 
-void DistributedForces::write_summed_scalar(std::ostream& os, PaddedRVecVector const& x) const
+void DistributedForces::write_summed_scalar(std::ostream& os, gmx::HostVector<gmx::RVec> const& x) const
 {
     for (size_t i = 0; i != summed.size(); ++i) {
         auto const& summed_i = summed[i];
@@ -155,7 +155,7 @@ void DistributedForces::write_scalar(std::ostream& os) const
     }
 }
 
-void DistributedForces::write_total_forces(std::ostream& os, PaddedRVecVector const& x) const
+void DistributedForces::write_total_forces(std::ostream& os, gmx::HostVector<gmx::RVec> const& x) const
 {
     std::vector<real> total_forces(syslen, 0.0);
     for (size_t i = 0; i != summed.size(); ++i) {
@@ -247,7 +247,7 @@ void DistributedForces::write_scalar_compat_ascii(std::ostream& os) const
     os << std::endl;
 }
 
-void DistributedForces::write_summed_compat_ascii(std::ostream& os, PaddedRVecVector const& x) const
+void DistributedForces::write_summed_compat_ascii(std::ostream& os, gmx::HostVector<gmx::RVec> const& x) const
 {
     // Print total number of interactions
     int nb_interactions = 0;
@@ -338,7 +338,7 @@ void DistributedForces::write_scalar_compat_bin(std::ostream& os) const
     }
 }
 
-void DistributedForces::write_summed_compat_bin(std::ostream& os, PaddedRVecVector const& x) const
+void DistributedForces::write_summed_compat_bin(std::ostream& os, gmx::HostVector<gmx::RVec> const& x) const
 {
     // Print total number of interactions
     int nb_interactions = 0;
@@ -392,7 +392,7 @@ void DistributedForces::scalar_real_divide(real divisor)
         for (auto& scalar_j : scalar_i) scalar_j.force *= inv;
 }
 
-void DistributedForces::summed_merge_to_scalar(PaddedRVecVector const& x)
+void DistributedForces::summed_merge_to_scalar(gmx::HostVector<gmx::RVec> const& x)
 {
     for (size_t i = 0; i != summed.size(); ++i) {
         auto & scalar_i = scalar[i];

src/gromacs/fda/DistributedForces.h

@@ -9,7 +9,7 @@
 #define SRC_GROMACS_FDA_DISTRIBUTEDFORCES_H_
 
 #include <vector>
-#include "gromacs/math/paddedvector.h"
+#include "gromacs/gpu_utils/hostallocator.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/utility/real.h"
 #include "DetailedForce.h"
@@ -55,28 +55,28 @@ class DistributedForces
 
     void write_detailed_vector(std::ostream& os) const;
 
-    void write_detailed_scalar(std::ostream& os, PaddedRVecVector const& x) const;
+    void write_detailed_scalar(std::ostream& os, gmx::HostVector<gmx::RVec> const& x) const;
 
     void write_summed_vector(std::ostream& os) const;
 
-    void write_summed_scalar(std::ostream& os, PaddedRVecVector const& x) const;
+    void write_summed_scalar(std::ostream& os, gmx::HostVector<gmx::RVec> const& x) const;
 
     void write_scalar(std::ostream& os) const;
 
-    void write_total_forces(std::ostream& os, PaddedRVecVector const& x) const;
+    void write_total_forces(std::ostream& os, gmx::HostVector<gmx::RVec> const& x) const;
 
     void write_scalar_compat_ascii(std::ostream& os) const;
 
-    void write_summed_compat_ascii(std::ostream& os, PaddedRVecVector const& x) const;
+    void write_summed_compat_ascii(std::ostream& os, gmx::HostVector<gmx::RVec> const& x) const;
 
     void write_scalar_compat_bin(std::ostream& os) const;
 
-    void write_summed_compat_bin(std::ostream& os, PaddedRVecVector const& x) const;
+    void write_summed_compat_bin(std::ostream& os, gmx::HostVector<gmx::RVec> const& x) const;
 
     /// Divide all scalar forces by the divisor
     void scalar_real_divide(real divisor);
 
-    void summed_merge_to_scalar(PaddedRVecVector const& x);
+    void summed_merge_to_scalar(gmx::HostVector<gmx::RVec> const& x);
 
 private:
 

src/gromacs/fda/FDA.cpp

@@ -406,13 +406,13 @@ void FDA::add_virial_dihedral(int i, int j, int k, int l,
     add_virial(l, v, QUARTER);
 }
 
-void FDA::save_and_write_scalar_time_averages(PaddedRVecVector const& x, gmx_mtop_t *mtop)
+void FDA::save_and_write_scalar_time_averages(gmx::HostVector<gmx::RVec> const& x, gmx_mtop_t *mtop)
 {
     if (fda_settings.time_averaging_period != 1) {
         if (atom_based.PF_or_PS_mode())
             atom_based.distributed_forces.summed_merge_to_scalar(x);
         if (residue_based.PF_or_PS_mode()) {
-        	PaddedRVecVector com = get_residues_com(x, mtop);
+        	gmx::HostVector<gmx::RVec> com = get_residues_com(x, mtop);
             residue_based.distributed_forces.summed_merge_to_scalar(com);
             for (int i = 0; i != fda_settings.syslen_residues; ++i) {
                 rvec_inc(time_averaging_com[i], com[i]);
@@ -458,7 +458,7 @@ void FDA::write_scalar_time_averages()
     time_averaging_steps = 0;
 }
 
-void FDA::write_frame(PaddedRVecVector const& x, gmx_mtop_t *mtop)
+void FDA::write_frame(gmx::HostVector<gmx::RVec> const& x, gmx_mtop_t *mtop)
 {
     atom_based.write_frame(x, nsteps);
     residue_based.write_frame(get_residues_com(x, mtop), nsteps);
@@ -685,7 +685,7 @@ void FDA::modify_energy_group_exclusions(gmx_mtop_t *mtop, t_inputrec *inputrec)
 
 }
 
-PaddedRVecVector FDA::get_residues_com(PaddedRVecVector const& x, gmx_mtop_t *mtop) const
+gmx::HostVector<gmx::RVec> FDA::get_residues_com(gmx::HostVector<gmx::RVec> const& x, gmx_mtop_t *mtop) const
 {
     int moltype_index, mol_index, d;
     int i, atom_index, atom_global_index, residue_global_index;
@@ -695,7 +695,7 @@ PaddedRVecVector FDA::get_residues_com(PaddedRVecVector const& x, gmx_mtop_t *mt
     rvec r;
 
     std::vector<real> mass(fda_settings.syslen_residues);
-    PaddedRVecVector com(fda_settings.syslen_residues);
+    gmx::HostVector<gmx::RVec> com(fda_settings.syslen_residues);
 
     for (i = 0; i < fda_settings.syslen_residues; i++) {
         mass[i] = 0.0;

src/gromacs/fda/FDA.h

@@ -16,7 +16,7 @@
 #include <vector>
 #include "FDABase.h"
 #include "FDASettings.h"
-#include "gromacs/math/paddedvector.h"
+#include "gromacs/gpu_utils/hostallocator.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "InteractionType.h"
 #include "PureInteractionType.h"
@@ -102,7 +102,7 @@ class FDA {
      * writing because for this fda->atoms would need to be initialized (to get the atom
      * number or to get the sys2ps mapping) which only happens when AtomBased is non-zero
      */
-    void save_and_write_scalar_time_averages(PaddedRVecVector const& x, gmx_mtop_t *mtop);
+    void save_and_write_scalar_time_averages(gmx::HostVector<gmx::RVec> const& x, gmx_mtop_t *mtop);
 
     /**
      * Write scalar time averages; this is similar to pf_write_frame, except that time averages are used
@@ -117,7 +117,7 @@ class FDA {
      */
     void write_scalar_time_averages();
 
-    void write_frame(PaddedRVecVector const& x, gmx_mtop_t *mtop);
+    void write_frame(gmx::HostVector<gmx::RVec> const& x, gmx_mtop_t *mtop);
 
     /// Main routine for FDA exclusions
     void modify_energy_group_exclusions(gmx_mtop_t *mtop, t_inputrec *inputrec) const;
@@ -132,7 +132,7 @@ class FDA {
      * not express the COM of the whole residue but the COM of the atoms of the residue which
      * are interesting for PF
      */
-    PaddedRVecVector get_residues_com(PaddedRVecVector const& x, gmx_mtop_t *mtop) const;
+    gmx::HostVector<gmx::RVec> get_residues_com(gmx::HostVector<gmx::RVec> const& x, gmx_mtop_t *mtop) const;
 
     /// Append group to energy groups, returns the position index
     int add_name_to_energygrp(char const* name, gmx_groups_t* groups) const;

src/gromacs/fda/FDABase.cpp

@@ -31,7 +31,7 @@ FDABase<Base>::FDABase(ResultType result_type, int syslen, std::string const& re
 }
 
 template <class Base>
-void FDABase<Base>::write_frame(PaddedRVecVector const& x, int nsteps)
+void FDABase<Base>::write_frame(gmx::HostVector<gmx::RVec> const& x, int nsteps)
 {
     switch (fda_settings.one_pair) {
         case OnePair::DETAILED:
@@ -94,7 +94,7 @@ void FDABase<Base>::write_frame(PaddedRVecVector const& x, int nsteps)
 }
 
 template <class Base>
-void FDABase<Base>::write_frame_detailed(PaddedRVecVector const& x, bool print_vector, int nsteps)
+void FDABase<Base>::write_frame_detailed(gmx::HostVector<gmx::RVec> const& x, bool print_vector, int nsteps)
 {
     result_file << "frame " << nsteps << std::endl;
     if (print_vector)
@@ -104,7 +104,7 @@ void FDABase<Base>::write_frame_detailed(PaddedRVecVector const& x, bool print_v
 }
 
 template <class Base>
-void FDABase<Base>::write_frame_summed(PaddedRVecVector const& x, bool print_vector, int nsteps)
+void FDABase<Base>::write_frame_summed(gmx::HostVector<gmx::RVec> const& x, bool print_vector, int nsteps)
 {
     result_file << "frame " << nsteps << std::endl;
     if (print_vector)
@@ -121,7 +121,7 @@ void FDABase<Base>::write_frame_scalar(int nsteps)
 }
 
 template <class Base>
-void FDABase<Base>::write_total_forces(PaddedRVecVector const& x)
+void FDABase<Base>::write_total_forces(gmx::HostVector<gmx::RVec> const& x)
 {
     distributed_forces.write_total_forces(result_file, x);
 }
@@ -162,7 +162,7 @@ void FDABase<Base>::write_frame_scalar_compat(int nsteps)
 }
 
 template <class Base>
-void FDABase<Base>::write_frame_summed_compat(PaddedRVecVector const& x, int nsteps)
+void FDABase<Base>::write_frame_summed_compat(gmx::HostVector<gmx::RVec> const& x, int nsteps)
 {
     if (result_type == ResultType::COMPAT_ASCII) {
         result_file << "<begin_block>" << std::endl;

src/gromacs/fda/FDABase.h

@@ -13,6 +13,7 @@
 #include <vector>
 #include "FDASettings.h"
 #include "DistributedForces.h"
+#include "gromacs/gpu_utils/hostallocator.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
 #include "OnePair.h"
@@ -78,17 +79,17 @@ class FDABase : Base
                result_type == ResultType::VIRIAL_STRESS_VON_MISES;
     }
 
-    void write_frame(PaddedRVecVector const& x, int nsteps);
+    void write_frame(gmx::HostVector<gmx::RVec> const& x, int nsteps);
 
-    void write_frame_detailed(PaddedRVecVector const& x, bool print_vector, int nsteps);
+    void write_frame_detailed(gmx::HostVector<gmx::RVec> const& x, bool print_vector, int nsteps);
 
-    void write_frame_summed(PaddedRVecVector const& x, bool print_vector, int nsteps);
+    void write_frame_summed(gmx::HostVector<gmx::RVec> const& x, bool print_vector, int nsteps);
 
     void write_frame_scalar(int nsteps);
 
-    void sum_total_forces(PaddedRVecVector const& x);
+    void sum_total_forces(gmx::HostVector<gmx::RVec> const& x);
 
-    void write_total_forces(PaddedRVecVector const& x);
+    void write_total_forces(gmx::HostVector<gmx::RVec> const& x);
 
     /**
      * Writes a header as in original PF implementation;
@@ -102,7 +103,7 @@ class FDABase : Base
 
     void write_frame_scalar_compat(int nsteps);
 
-    void write_frame_summed_compat(PaddedRVecVector const& x, int nsteps);
+    void write_frame_summed_compat(gmx::HostVector<gmx::RVec> const& x, int nsteps);
 
     /// The stress is the negative atom_vir value.
     void write_virial_sum();

src/gromacs/fda/Utilities.cpp

@@ -37,7 +37,7 @@ real vector2signedscalar(const rvec v, const rvec xi, const rvec xj, Vector2Scal
     return GMX_FLOAT_MAX;
 }
 
-real vector2unsignedscalar(const rvec v, int i, int j, PaddedRVecVector const& x)
+real vector2unsignedscalar(const rvec v, int i, int j, gmx::HostVector<gmx::RVec> const& x)
 {
     rvec r;
     rvec_sub(x[j], x[i], r);

src/gromacs/fda/Utilities.h

@@ -8,7 +8,7 @@
 #ifndef SRC_GROMACS_FDA_UTILITIES_H_
 #define SRC_GROMACS_FDA_UTILITIES_H_
 
-#include "gromacs/math/paddedvector.h"
+#include "gromacs/gpu_utils/hostallocator.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/utility/real.h"
 #include "Vector2Scalar.h"
@@ -23,7 +23,7 @@ namespace fda {
  */
 real vector2signedscalar(const rvec v, const rvec xi, const rvec xj, Vector2Scalar v2s);
 
-real vector2unsignedscalar(const rvec v, int i, int j, PaddedRVecVector const& x);
+real vector2unsignedscalar(const rvec v, int i, int j, gmx::HostVector<gmx::RVec> const& x);
 
 } // namespace fda