Commit 13be8085 authored by Anne Gunn's avatar Anne Gunn
Browse files

T2345: Replace instances of NULL with nullptr 

Per guidance from Axel, revert lib/kokkos and lib/colvars
to remove nullptr changes.
parent f1ef7d85

lib/colvars/colvar.cpp

+10 −10
Original line number Diff line number Diff line
@@ -22,7 +22,7 @@ 


colvar::colvar()

{

  runave_os = nullptr;

  runave_os = NULL;



  prev_timestep = -1L;

  after_restart = false;
@@ -62,7 +62,7 @@ int colvar::init(std::string const &conf) 
  get_keyval(conf, "name", this->name,

             (std::string("colvar")+cvm::to_str(cv->variables()->size())));



  if ((cvm::colvar_by_name(this->name) != nullptr) &&

  if ((cvm::colvar_by_name(this->name) != NULL) &&

      (cvm::colvar_by_name(this->name) != this)) {

    cvm::error("Error: this colvar cannot have the same name, \""+this->name+

                      "\", as another colvar.\n",
@@ -744,7 +744,7 @@ template<typename def_class_name> int colvar::init_components_type(std::string c 
              : ".\n"));

    cvm::increase_depth();

    cvc *cvcp = new def_class_name(def_conf);

    if (cvcp != nullptr) {

    if (cvcp != NULL) {

      cvcs.push_back(cvcp);

      cvcp->check_keywords(def_conf, def_config_key);

      cvcp->config_key = def_config_key;
@@ -994,7 +994,7 @@ int colvar::parse_analysis(std::string const &conf) 
      acf_type = acf_vel;

      enable(f_cv_fdiff_velocity);

      colvar *cv2 = cvm::colvar_by_name(acf_colvar_name);

      if (cv2 == nullptr) {

      if (cv2 == NULL) {

        return cvm::error("Error: collective variable \""+acf_colvar_name+

                          "\" is not defined at this time.\n", INPUT_ERROR);

      }
@@ -1215,14 +1215,14 @@ colvar::~colvar() 
  for (std::vector<Lepton::CompiledExpression *>::iterator cei = value_evaluators.begin();

       cei != value_evaluators.end();

       ++cei) {

    if (*cei != nullptr) delete (*cei);

    if (*cei != NULL) delete (*cei);

  }

  value_evaluators.clear();



  for (std::vector<Lepton::CompiledExpression *>::iterator gei = gradient_evaluators.begin();

       gei != gradient_evaluators.end();

       ++gei) {

    if (*gei != nullptr) delete (*gei);

    if (*gei != NULL) delete (*gei);

  }

  gradient_evaluators.clear();

#endif
@@ -1972,7 +1972,7 @@ void const *colvar::get_cvc_param_ptr(std::string const &param_name) 
  }

  cvm::error("Error: calling colvar::get_cvc_param() for a variable "

             "with more than one component.\n", COLVARS_NOT_IMPLEMENTED);

  return nullptr;

  return NULL;

}
@@ -1983,7 +1983,7 @@ colvarvalue const *colvar::get_cvc_param_grad(std::string const &param_name) 
  }

  cvm::error("Error: calling colvar::get_cvc_param_grad() for a variable "

             "with more than one component.\n", COLVARS_NOT_IMPLEMENTED);

  return nullptr;

  return NULL;

}
@@ -2422,7 +2422,7 @@ int colvar::calc_acf() 
  // the pointer to each vector is changed at every step



  colvar const *cfcv = cvm::colvar_by_name(acf_colvar_name);

  if (cfcv == nullptr) {

  if (cfcv == NULL) {

    return cvm::error("Error: collective variable \""+acf_colvar_name+

                      "\" is not defined at this time.\n", INPUT_ERROR);

  }
@@ -2660,7 +2660,7 @@ int colvar::calc_runave() 


      if ((*x_history_p).size() >= runave_length-1) {



        if (runave_os == nullptr) {

        if (runave_os == NULL) {

          if (runave_outfile.size() == 0) {

            runave_outfile = std::string(cvm::output_prefix()+"."+

                                         this->name+".runave.traj");

lib/colvars/colvaratoms.cpp

+4 −4
Original line number Diff line number Diff line
@@ -105,7 +105,7 @@ cvm::atom_group::~atom_group() 


  if (fitting_group) {

    delete fitting_group;

    fitting_group = nullptr;

    fitting_group = NULL;

  }



  cvm::main()->unregister_named_atom_group(this);
@@ -217,7 +217,7 @@ int cvm::atom_group::init() 
  b_center = false;

  b_rotate = false;

  b_user_defined_fit = false;

  fitting_group = nullptr;

  fitting_group = NULL;



  noforce = false;
@@ -368,7 +368,7 @@ int cvm::atom_group::parse(std::string const &group_conf) 


  // Optional group name will let other groups reuse atom definition

  if (get_keyval(group_conf, "name", name)) {

    if ((cvm::atom_group_by_name(this->name) != nullptr) &&

    if ((cvm::atom_group_by_name(this->name) != NULL) &&

        (cvm::atom_group_by_name(this->name) != this)) {

      cvm::error("Error: this atom group cannot have the same name, \""+this->name+

                        "\", as another atom group.\n",
@@ -395,7 +395,7 @@ int cvm::atom_group::parse(std::string const &group_conf) 
    std::string atoms_of = "";

    if (get_keyval(group_conf, "atomsOfGroup", atoms_of)) {

      atom_group * ag = atom_group_by_name(atoms_of);

      if (ag == nullptr) {

      if (ag == NULL) {

        cvm::error("Error: cannot find atom group with name " + atoms_of + ".\n");

        return COLVARS_ERROR;

      }

lib/colvars/colvarbias.cpp

+13 −13
Original line number Diff line number Diff line
@@ -47,7 +47,7 @@ int colvarbias::init(std::string const &conf) 


    {

      colvarbias *bias_with_name = cvm::bias_by_name(this->name);

      if (bias_with_name != nullptr) {

      if (bias_with_name != NULL) {

        if ((bias_with_name->rank != this->rank) ||

            (bias_with_name->bias_type != this->bias_type)) {

          cvm::error("Error: this bias cannot have the same name, \""+this->name+
@@ -295,8 +295,8 @@ int colvarbias::update() 
    colvar_values[i] = colvars[i]->value();

  }



  error_code |= calc_energy(nullptr);

  error_code |= calc_forces(nullptr);

  error_code |= calc_energy(NULL);

  error_code |= calc_forces(NULL);



  return error_code;

}
@@ -547,8 +547,8 @@ colvarbias_ti::colvarbias_ti(char const *key) 
  : colvarbias(key)

{

  provide(f_cvb_calc_ti_samples);

  ti_avg_forces = nullptr;

  ti_count = nullptr;

  ti_avg_forces = NULL;

  ti_count = NULL;

}
@@ -560,13 +560,13 @@ colvarbias_ti::~colvarbias_ti() 


int colvarbias_ti::clear_state_data()

{

  if (ti_avg_forces != nullptr) {

  if (ti_avg_forces != NULL) {

    delete ti_avg_forces;

    ti_avg_forces = nullptr;

    ti_avg_forces = NULL;

  }

  if (ti_count != nullptr) {

  if (ti_count != NULL) {

    delete ti_count;

    ti_count = nullptr;

    ti_count = NULL;

  }

  return COLVARS_OK;

}
@@ -622,7 +622,7 @@ int colvarbias_ti::init(std::string const &conf) 
int colvarbias_ti::init_grids()

{

  if (is_enabled(f_cvb_calc_ti_samples)) {

    if (ti_avg_forces == nullptr) {

    if (ti_avg_forces == NULL) {

      ti_bin.resize(num_variables());

      ti_system_forces.resize(num_variables());

      for (size_t icv = 0; icv < num_variables(); icv++) {
@@ -643,7 +643,7 @@ int colvarbias_ti::init_grids() 


int colvarbias_ti::update()

{

  return update_system_forces(nullptr);

  return update_system_forces(NULL);

}
@@ -679,7 +679,7 @@ int colvarbias_ti::update_system_forces(std::vector<colvarvalue> const 
          ti_system_forces[i] = variables(i)->total_force();

        } else {

          ti_system_forces[i] = variables(i)->total_force() -

            ((subtract_forces != nullptr) ?

            ((subtract_forces != NULL) ?

             (*subtract_forces)[i] : previous_colvar_forces[i]);

        }

      }
@@ -759,7 +759,7 @@ int colvarbias_ti::write_output_files() 


  std::string const ti_output_prefix = cvm::output_prefix()+"."+this->name;



  std::ostream *os = nullptr;

  std::ostream *os = NULL;



  if (is_enabled(f_cvb_write_ti_samples)) {

    std::string const ti_count_file_name(ti_output_prefix+".ti.count");

lib/colvars/colvarbias.h

+2 −2
Original line number Diff line number Diff line
@@ -58,12 +58,12 @@ public: 
  virtual int update();



  /// Compute the energy of the bias

  /// Uses the vector of colvar values provided if not nullptr, and the values

  /// Uses the vector of colvar values provided if not NULL, and the values

  /// currently cached in the bias instance otherwise

  virtual int calc_energy(std::vector<colvarvalue> const *values);



  /// Compute the forces due to the bias

  /// Uses the vector of colvar values provided if not nullptr, and the values

  /// Uses the vector of colvar values provided if not NULL, and the values

  /// currently cached in the bias instance otherwise

  virtual int calc_forces(std::vector<colvarvalue> const *values);

lib/colvars/colvarbias_abf.cpp

+21 −21
Original line number Diff line number Diff line
@@ -18,16 +18,16 @@ colvarbias_abf::colvarbias_abf(char const *key) 
    b_UI_estimator(false),

    b_CZAR_estimator(false),

    pabf_freq(0),

    system_force(nullptr),

    gradients(nullptr),

    samples(nullptr),

    pmf(nullptr),

    z_gradients(nullptr),

    z_samples(nullptr),

    czar_gradients(nullptr),

    czar_pmf(nullptr),

    last_gradients(nullptr),

    last_samples(nullptr)

    system_force(NULL),

    gradients(NULL),

    samples(NULL),

    pmf(NULL),

    z_gradients(NULL),

    z_samples(NULL),

    czar_gradients(NULL),

    czar_pmf(NULL),

    last_gradients(NULL),

    last_samples(NULL)

{

}
@@ -261,37 +261,37 @@ colvarbias_abf::~colvarbias_abf() 
{

  if (samples) {

    delete samples;

    samples = nullptr;

    samples = NULL;

  }



  if (gradients) {

    delete gradients;

    gradients = nullptr;

    gradients = NULL;

  }



  if (pmf) {

    delete pmf;

    pmf = nullptr;

    pmf = NULL;

  }



  if (z_samples) {

    delete z_samples;

    z_samples = nullptr;

    z_samples = NULL;

  }



  if (z_gradients) {

    delete z_gradients;

    z_gradients = nullptr;

    z_gradients = NULL;

  }



  if (czar_gradients) {

    delete czar_gradients;

    czar_gradients = nullptr;

    czar_gradients = NULL;

  }



  if (czar_pmf) {

    delete czar_pmf;

    czar_pmf = nullptr;

    czar_pmf = NULL;

  }



  // shared ABF
@@ -299,17 +299,17 @@ colvarbias_abf::~colvarbias_abf() 
  // but now we can call shared externally

  if (last_samples) {

    delete last_samples;

    last_samples = nullptr;

    last_samples = NULL;

  }



  if (last_gradients) {

    delete last_gradients;

    last_gradients = nullptr;

    last_gradients = NULL;

  }



  if (system_force) {

    delete [] system_force;

    system_force = nullptr;

    system_force = NULL;

  }

}
@@ -488,7 +488,7 @@ int colvarbias_abf::update() 
  }



  /// Add the bias energy for 1D ABF

  bias_energy = calc_energy(nullptr);

  bias_energy = calc_energy(NULL);



  return COLVARS_OK;

}

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