llnl · siuwuncheung · Mar 25, 2025 · Sep 26, 2024 · Sep 30, 2024 · Sep 30, 2024
diff --git a/src/BlockVector.cc b/src/BlockVector.cc
@@ -209,7 +209,7 @@ void BlockVector<ScalarType, MemorySpaceType>::allocate_storage()
         std::cerr << "ERROR BlockVector: trying to use allocation "
                   << size_storage_ << " bigger than initialy preallocated "
                   << allocated_size_storage_ << "!!!" << std::endl;
-        ct.global_exit(0);
+        ct.global_exit();
     }
     storage_ = class_storage_[my_allocation_];
     assert(class_storage_.size() > 0);

diff --git a/src/Control.cc b/src/Control.cc
@@ -495,7 +495,7 @@ void Control::sync(void)
         if (mpirc != MPI_SUCCESS)
         {
             (*MPIdata::sout) << "MPI Bcast of Control failed!!!" << std::endl;
-            MPI_Abort(comm_global_, 2);
+            MPI_Abort(comm_global_, EXIT_FAILURE);
         }
     };
 
@@ -1152,7 +1152,7 @@ void Control::setTolEigenvalueGram(const float tol)
                          << threshold_eigenvalue_gram_ << std::endl;
 }
 
-void Control::global_exit(int i) { MPI_Abort(comm_global_, i); }
+void Control::global_exit() { MPI_Abort(comm_global_, EXIT_FAILURE); }
 
 void Control::setSpecies(Potentials& pot)
 {
@@ -1342,7 +1342,7 @@ void Control::setOptions(const boost::program_options::variables_map& vm)
             (*MPIdata::serr)
                 << "ERROR in Control::setOptions: Invalid restart dump type"
                 << std::endl;
-            MPI_Abort(comm_global_, 2);
+            MPI_Abort(comm_global_, EXIT_FAILURE);
         }
 
         (*MPIdata::sout) << "Output restart file: " << out_restart_file
@@ -1549,14 +1549,14 @@ void Control::setOptions(const boost::program_options::variables_map& vm)
             else
             {
                 std::cerr << "ERROR: Spread Penalty needs a type" << std::endl;
-                MPI_Abort(comm_global_, 0);
+                MPI_Abort(comm_global_, EXIT_FAILURE);
             }
 
             if (spread_penalty_target_ <= 0.)
             {
                 (*MPIdata::sout) << "Invalid value for Spread Penalty target: "
                                  << spread_penalty_target_ << std::endl;
-                MPI_Abort(comm_global_, 0);
+                MPI_Abort(comm_global_, EXIT_FAILURE);
             }
         }
 
@@ -1599,7 +1599,7 @@ void Control::setOptions(const boost::program_options::variables_map& vm)
                 {
                     (*MPIdata::sout) << "Invalid value for Thermostat.type: "
                                      << thermostat_type << std::endl;
-                    MPI_Abort(comm_global_, 0);
+                    MPI_Abort(comm_global_, EXIT_FAILURE);
                 }
 
                 tkel = vm["Thermostat.temperature"].as<float>();
@@ -1608,15 +1608,15 @@ void Control::setOptions(const boost::program_options::variables_map& vm)
                     (*MPIdata::sout)
                         << "Invalid value for Thermostat.temperature: " << tkel
                         << std::endl;
-                    MPI_Abort(comm_global_, 0);
+                    MPI_Abort(comm_global_, EXIT_FAILURE);
                 }
                 thtime = vm["Thermostat.relax_time"].as<float>();
                 if (thtime < 0.)
                 {
                     (*MPIdata::sout)
                         << "Invalid value for Thermostat.relax_time: " << thtime
                         << std::endl;
-                    MPI_Abort(comm_global_, 0);
+                    MPI_Abort(comm_global_, EXIT_FAILURE);
                 }
 
                 if (str.compare("SCALING") == 0)
@@ -1627,7 +1627,7 @@ void Control::setOptions(const boost::program_options::variables_map& vm)
                         (*MPIdata::sout)
                             << "Invalid value for Thermostat.width: " << thwidth
                             << std::endl;
-                        MPI_Abort(comm_global_, 0);
+                        MPI_Abort(comm_global_, EXIT_FAILURE);
                     }
                 }
             }

diff --git a/src/Control.h b/src/Control.h
@@ -353,7 +353,7 @@ class Control
         return pair_mlwf_distance_threshold_;
     }
 
-    void global_exit(int i);
+    void global_exit();
 
     bool Mehrstellen() const { return (lap_type == 0 || lap_type == 10); }
 

diff --git a/src/DistMatrix/BlacsContext.cc b/src/DistMatrix/BlacsContext.cc
@@ -191,7 +191,7 @@ BlacsContext::BlacsContext(
     {
         std::cerr << " BlacsContext::BlacsContext: type = " << type
                   << " is an incorrect parameter" << std::endl;
-        MPI_Abort(comm_global, 0);
+        MPI_Abort(comm_global, EXIT_FAILURE);
     }
 
     size_ = nprow_ * npcol_;
@@ -222,7 +222,7 @@ BlacsContext::BlacsContext(
     {
         std::cerr << " nprocs_=" << nprocs_ << std::endl;
         std::cerr << " BlacsContext nprow*npcol > nprocs_" << std::endl;
-        MPI_Abort(comm_global, 0);
+        MPI_Abort(comm_global, EXIT_FAILURE);
     }
 
     ictxt_ = Csys2blacs_handle(comm_global_);
@@ -252,7 +252,7 @@ BlacsContext::BlacsContext(
     {
         std::cerr << " BlacsContext::BlacsContext: invalid parameters"
                   << " in " << __FILE__ << ":" << __LINE__ << std::endl;
-        MPI_Abort(comm_global, 0);
+        MPI_Abort(comm_global, EXIT_FAILURE);
     }
     int* pmap = new int[nprow * npcol];
     // build pmap
@@ -296,7 +296,7 @@ BlacsContext::BlacsContext(BlacsContext& bc, const int irow, const int icol,
     {
         std::cerr << " BlacsContext::BlacsContext: invalid parameters"
                   << std::endl;
-        MPI_Abort(comm_global_, 0);
+        MPI_Abort(comm_global_, EXIT_FAILURE);
     }
     int* pmap = new int[nprow * npcol];
     // build pmap
@@ -350,7 +350,7 @@ BlacsContext::BlacsContext(const BlacsContext& bc, const char type)
         std::cerr
             << " BlacsContext::BlacsContext: row/col incorrect parameter: "
             << type << std::endl;
-        MPI_Abort(comm_global_, 0);
+        MPI_Abort(comm_global_, EXIT_FAILURE);
     }
 
     ictxt_ = Csys2blacs_handle(comm_global_);

diff --git a/src/DistMatrix/DistMatrix.h b/src/DistMatrix/DistMatrix.h
@@ -28,7 +28,7 @@
     std::cerr << "ERROR in file " << __FILE__ << " at line " << __LINE__       \
               << std::endl;                                                    \
     std::cerr << "Error Message: " << X << std::endl;                          \
-    MPI_Abort(comm_global_, 2);
+    MPI_Abort(comm_global_, EXIT_FAILURE);
 
 #endif
 

diff --git a/src/DistanceConstraint.cc b/src/DistanceConstraint.cc
@@ -99,7 +99,7 @@ bool DistanceConstraint::enforce(void)
     {
         cerr << "mype=" << mype << ", tau1p_[0]=" << tau1p_[0] << endl;
         cerr << "mype=" << mype << ", tau2p_[0]=" << tau2p_[0] << endl;
-        MPI_Abort(MPI_COMM_WORLD, 0);
+        MPI_Abort(MPI_COMM_WORLD, EXIT_FAILURE);
     }
     if (locally_owned_)
         (*MPIdata::sout) << setprecision(8) << "DistanceConstraint, d=" << d

diff --git a/src/Electrostatic.cc b/src/Electrostatic.cc
@@ -65,7 +65,7 @@ Electrostatic::~Electrostatic()
     if (grhoc_ != nullptr) delete grhoc_;
 }
 
-void Electrostatic::setupInitialVh(const POTDTYPE* const vh_init)
+void Electrostatic::setupInitialVh(const std::vector<POTDTYPE>& vh_init)
 {
     poisson_solver_->set_vh(vh_init);
 
@@ -153,7 +153,7 @@ void Electrostatic::setupPB(
 
     // initialize vh with last trial solution
     pb::GridFunc<POTDTYPE> gf_vh(*pbGrid_, bc_[0], bc_[1], bc_[2]);
-    gf_vh.assign(pot.vh_rho());
+    gf_vh.assign((pot.vh_rho()).data());
     poisson_solver_->set_vh(gf_vh);
 }
 

diff --git a/src/Electrostatic.h b/src/Electrostatic.h
@@ -63,7 +63,7 @@ class Electrostatic
     template <class T>
     void computeVh(const pb::GridFunc<POTDTYPE>& vhinit, const Ions& ions,
         Rho<T>& rho, Potentials& pot);
-    void setupInitialVh(const POTDTYPE* const);
+    void setupInitialVh(const std::vector<POTDTYPE>&);
     void setupInitialVh(const pb::GridFunc<POTDTYPE>&);
     template <class T>
     void computeVhRho(Rho<T>& rho);

diff --git a/src/ExtendedGridOrbitals.cc b/src/ExtendedGridOrbitals.cc
@@ -1239,7 +1239,7 @@ double ExtendedGridOrbitals::dotProduct(
                             "dot product type"
                          << std::endl;
         Control& ct = *(Control::instance());
-        ct.global_exit(2);
+        ct.global_exit();
     }
 
     dot_product_tm_.stop();

diff --git a/src/Forces.cc b/src/Forces.cc
@@ -272,9 +272,10 @@ void Forces<T>::get_loc_proj(RHODTYPE* rho,
     const int numpt = mymesh->numpt();
 
     Potentials& pot = hamiltonian_->potential();
+    const std::vector<POTDTYPE>& vh_rho(pot.vh_rho());
     for (int idx = 0; idx < numpt; idx++)
     {
-        const double vhrho = pot.vh_rho(idx);
+        const double vhrho = vh_rho[idx];
         for (short dir = 0; dir < 3; dir++)
         {
             double* lproj = &(loc_proj[dir * NPTS]);

diff --git a/src/HDFrestart.cc b/src/HDFrestart.cc
@@ -1440,8 +1440,8 @@ int HDFrestart::read_1func_hdf5(T* vv, const std::string& datasetname)
 }
 
 template <class T>
-int HDFrestart::write_1func_hdf5(
-    T* vv, const std::string& datasetname, double* ll, double* cell_origin)
+int HDFrestart::write_1func_hdf5(const T* const vv,
+    const std::string& datasetname, double* ll, double* cell_origin)
 {
     assert(ll != nullptr);
     assert(cell_origin != nullptr);
@@ -1652,7 +1652,7 @@ int HDFrestart::readData(
 }
 
 template <class T>
-int HDFrestart::writeData(T* data, hid_t space_id, hid_t memspace,
+int HDFrestart::writeData(const T* const data, hid_t space_id, hid_t memspace,
     hid_t dset_id, const short precision)
 {
     if (precision == 1)
@@ -1922,10 +1922,12 @@ int HDFrestart::readAtomicData(std::string datasetname, std::vector<int>& data)
     // send data to inactive PEs
     if (gather_data_x_) gatherDataXdir(data);
 
+#ifdef MGMOL_USE_HDF5P
     if (useHdf5p())
     {
         data.erase(std::remove(data.begin(), data.end(), -1), data.end());
     }
+#endif
 
     return 0;
 }
@@ -1974,10 +1976,12 @@ int HDFrestart::readAtomicData(
         }
     }
 
+#ifdef MGMOL_USE_HDF5P
     if (useHdf5p())
     {
         data.erase(std::remove(data.begin(), data.end(), 1e+32), data.end());
     }
+#endif
     if (gather_data_x_) gatherDataXdir(data);
 
     return 0;
@@ -2017,7 +2021,8 @@ int HDFrestart::readAtomicData(
 {
     Control& ct = *(Control::instance());
     if (onpe0 && ct.verbose > 0)
-        (*MPIdata::sout) << "HDFrestart::readAtomicNames()..." << std::endl;
+        (*MPIdata::sout) << "HDFrestart::readAtomicData(), dataset = "
+                         << datasetname << std::endl;
 
     std::vector<char> buffer;
     short name_length = 7; // default, value used before February 2016
@@ -2095,19 +2100,19 @@ int HDFrestart::readAtomicData(
     {
         std::string t(&buffer[i], name_length);
         assert(t.size() > 0);
-        // cout<<"name="<<t<<endl;
 
         stripLeadingAndTrailingBlanks(t);
-        // cout<<"stripped name="<<t<<endl;
+        // std::cout<<"stripped name="<<t<<std::endl;
 
-        assert(t.size() > 0);
         data.push_back(t);
     }
 
+#ifdef MGMOL_USE_HDF5P
     if (useHdf5p())
     {
         data.erase(std::remove(data.begin(), data.end(), ""), data.end());
     }
+#endif
 
     return 0;
 }
@@ -2232,13 +2237,13 @@ template int HDFrestart::read_1func_hdf5(float*, const std::string&);
 template int HDFrestart::read_1func_hdf5(double*, const std::string&);
 
 template int HDFrestart::write_1func_hdf5(
-    double*, const std::string&, double* ll, double* origin);
+    const double* const, const std::string&, double* ll, double* origin);
 
 template int HDFrestart::readData(
     double*, hid_t memspace, hid_t dset_id, const short precision);
 template int HDFrestart::readData(
     float*, hid_t memspace, hid_t dset_id, const short precision);
-template int HDFrestart::writeData(double* vv, hid_t filespace, hid_t memspace,
-    hid_t dset_id, const short precision);
-template int HDFrestart::writeData(float* vv, hid_t filespace, hid_t memspace,
-    hid_t dset_id, const short precision);
+template int HDFrestart::writeData(const double* const vv, hid_t filespace,
+    hid_t memspace, hid_t dset_id, const short precision);
+template int HDFrestart::writeData(const float* const vv, hid_t filespace,
+    hid_t memspace, hid_t dset_id, const short precision);
diff --git a/src/HDFrestart.h b/src/HDFrestart.h
@@ -246,16 +246,16 @@ class HDFrestart
     int read_1func_hdf5(T*, const std::string&);
 
     template <class T>
-    int write_1func_hdf5(
-        T*, const std::string&, double* ll = nullptr, double* origin = nullptr);
+    int write_1func_hdf5(const T* const, const std::string&,
+        double* ll = nullptr, double* origin = nullptr);
 
     int read_att(const hid_t dset_id, const std::string& attname,
         std::vector<double>& attr_data);
 
     // write data in file with precision "precision"
     template <class T>
-    int writeData(T* vv, hid_t filespace, hid_t memspace, hid_t dset_id,
-        const short precision);
+    int writeData(const T* const vv, hid_t filespace, hid_t memspace,
+        hid_t dset_id, const short precision);
 
     template <class T>
     int readData(T* vv, hid_t memspace, hid_t dset_id, const short precision);

diff --git a/src/Ion.cc b/src/Ion.cc
@@ -294,12 +294,18 @@ void Ion::getIonData(IonData& idata) const
     }
 }
 
+void Ion::resetPositionsToPrevious()
+{
+    for (int pos = 0; pos < 3; pos++)
+        position_[pos] = old_position_[pos];
+}
+
 void Ion::setFromIonData(const IonData& data)
 {
     // random state
     setRandomState(data.rand_state[0], data.rand_state[1], data.rand_state[2]);
     // previous position
-    setOldPosition(
+    setPreviousPosition(
         data.old_position[0], data.old_position[1], data.old_position[2]);
     // velocity
     setVelocity(data.velocity[0], data.velocity[1], data.velocity[2]);

diff --git a/src/Ion.h b/src/Ion.h
@@ -74,12 +74,6 @@ class Ion
 
         position_[i] += shift;
     }
-    void setOldPosition(const double x, const double y, const double z)
-    {
-        old_position_[0] = x;
-        old_position_[1] = y;
-        old_position_[2] = z;
-    }
 
 public:
     Ion(const Species& species, const std::string& name, const double crds[3],
@@ -96,6 +90,13 @@ class Ion
     void init(const double crds[3], const double velocity[3], const bool lock);
     void setup();
 
+    void setPreviousPosition(const double x, const double y, const double z)
+    {
+        old_position_[0] = x;
+        old_position_[1] = y;
+        old_position_[2] = z;
+    }
+
     std::shared_ptr<KBprojector> kbproj() { return kbproj_; }
     const std::shared_ptr<KBprojector> kbproj() const { return kbproj_; }
 
@@ -189,6 +190,9 @@ class Ion
 
         kbproj_->clear();
     }
+
+    void resetPositionsToPrevious();
+
     void shiftPositionXLBOMDTest(Vector3D shift)
     {
         for (short dir = 0; dir < 3; dir++)

diff --git a/src/IonicAlgorithm.cc b/src/IonicAlgorithm.cc
@@ -57,7 +57,7 @@ void IonicAlgorithm<OrbitalsType>::init(HDFrestart* h5f_file)
     if (ct.restart_info > 0)
     {
         int status = stepper_->init(*h5f_file);
-        if (status < 0) ct.global_exit(2);
+        if (status < 0) ct.global_exit();
 
         // if restart data for lbfgs found
         if (status == 0)