AMS_IO Class Reference

#include <AMS_IO.h>

Inheritance diagram for AMS_IO:

Public Member Functions
	AMS_IO (const Parameters &p)
	~AMS_IO ()
void	initialize ()
void	cleanMemory (void)
void	force (long N, const double *R, const int *atomicNrs, double *F, double *U, double *variance, const double *box)
Public Member Functions inherited from eonc::Potential
	Potential (PotType a_ptype)
	Potential (PotType a_ptype, const Parameters &)
	Potential (const Parameters &a_params)
virtual	~Potential ()
std::tuple< double, AtomMatrix >	get_ef (const AtomMatrix &pos, const VectorXi &atmnrs, const Matrix3d &box)
PotType	getType () const
virtual bool	isSurrogate () const noexcept
	Whether this is a surrogate (GP) potential.
virtual bool	requiresIsolatedMoleculeLayout () const noexcept
	True for molecular QM / non-PBC backends (NWChem socket, ASE ORCA/NWChem, …).
virtual bool	isThreadSafe () const noexcept
	Whether this potential's force() can be called from multiple threads on the SAME instance.
virtual bool	isSharedInstanceThreadSafe () const noexcept
	Conservative gate for sharing one Potential instance across threads.
virtual bool	needsPerImageInstance () const noexcept
	Whether NEB should create separate Potential instances per image for true parallel force evaluation.
virtual bool	supportsBatchEvaluation () const noexcept
	Whether this potential supports batched evaluation of N systems in a single call.
virtual void	forceBatch (long nSystems, long nAtoms, const double *const *positions, const int *const *atomicNrs, double *const *forces, double *energies, double *variances, const double *const *boxes)
	Evaluate forces for N systems in a single call.

Private Member Functions
void	passToSystem (long N, const double *R, const int *atomicNrs, const double *box)
void	recieveFromSystem (long N, double *F, double *U)

Private Attributes
std::string	engine
std::string	model
std::string	forcefield
std::string	xc

Additional Inherited Members
Public Attributes inherited from eonc::Potential
std::atomic< size_t >	forceCallCounter
Protected Attributes inherited from eonc::Potential
PotType	ptype

Detailed Description

Definition at line 19 of file AMS_IO.h.

Constructor & Destructor Documentation

AMS_IO()

AMS_IO::AMS_IO

(

const Parameters &

p

)

Definition at line 48 of file AMS_IO.cpp.

    : Potential(PotType::AMS_IO, p) {
  engine = p.ams_options.engine;
  forcefield = p.ams_options.forcefield;
  model = p.ams_options.model;
  xc = p.ams_options.xc;
  return;
}

~AMS_IO()

AMS_IO::~AMS_IO

(

)

Definition at line 59 of file AMS_IO.cpp.

{ cleanMemory(); }

Member Function Documentation

cleanMemory()

void AMS_IO::cleanMemory

(

void

)

Definition at line 57 of file AMS_IO.cpp.

{ return; }

force()

void AMS_IO::force ( long N, const double * R, const int * atomicNrs, double * F, double * U, double * variance, const double * box )

virtual

Implements eonc::Potential.

Definition at line 101 of file AMS_IO.cpp.

                                                                   {
  variance = nullptr;
  passToSystem(N, R, atomicNrs, box);
  // Run a single point AMS_IO calculation and write the results into
  // ams_output
  eonc::pot::runOrThrow(kRunCommand);
  recieveFromSystem(N, F, U);
  return;
}

initialize()

void AMS_IO::initialize ( )

inline

Definition at line 24 of file AMS_IO.h.

{};

passToSystem()

void AMS_IO::passToSystem ( long N, const double * R, const int * atomicNrs, const double * box )

private

Definition at line 112 of file AMS_IO.cpp.

{
  std::ofstream out(kRunScript, std::ios::trunc);
  if (!out) {
    throw std::runtime_error(
        std::format("Could not open {} for writing", kRunScript));
  }
 
  out << "#!/bin/sh\n";
  out << "ams --delete-old-results <<eor\n";
  out << "Task SinglePoint\n";
  out << "System\n";
  out << " Atoms\n";
  for (long i = 0; i < N; i++) {
    out << std::format("  {}\t{:.19f}\t{:.19f}\t{:.19f}\n",
                       atomicNumber2symbol(atomicNrs[i]), R[i * 3 + 0],
                       R[i * 3 + 1], R[i * 3 + 2]);
  }
  out << " End\n";
  if (!model.empty() || !forcefield.empty()) {
    out << " Lattice\n";
    for (int i = 0; i < 3; i++) {
      out << std::format("  {:.19f}\t{:.19f}\t{:.19f}\n", box[i * 3 + 0],
                         box[i * 3 + 1], box[i * 3 + 2]);
    }
    out << " End\n";
  }
  out << "End\n";
  out << std::format("Engine {}\n", engine);
  if (!forcefield.empty()) {
    out << std::format("     Forcefield {}\n", forcefield);
  }
  if (!model.empty()) {
    out << std::format("     Model {}\n", model);
  }
  if (!xc.empty()) {
    out << std::format("xc {}\n", xc);
    // basis set not specified (default = DZ)
    out << std::format("     hybrid {}\n", xc);
    out << "end\n";
  }
  out << "EndEngine\n";
  out << "Properties\n";
  out << " Gradients\n";
  out << "End\n";
  out << "eor";
 
  out.close();
  if (!out) {
    throw std::runtime_error(
        std::format("Could not write the AMS input to {}", kRunScript));
  }
 
#ifndef _WIN32
  if (chmod(kRunScript, S_IRWXU) != 0) {
    throw std::runtime_error(
        std::format("Could not make {} executable", kRunScript));
  }
#endif
  return;
}

recieveFromSystem()

void AMS_IO::recieveFromSystem ( long N, double * F, double * U )

private

Definition at line 176 of file AMS_IO.cpp.

                                                           {
  std::ifstream in(kOutputFile);
  if (!in) {
    throw std::runtime_error(
        std::format("Could not open {}; AMS left no output", kOutputFile));
  }
 
  bool haveEnergy = false;
  bool haveGradients = false;
  std::string line;
 
  while (std::getline(in, line)) {
 
    if (line == kEnergyMarker) { // Finding the Energy in the output file
      std::string junk;
      if (!(in >> junk >> junk >> junk >> *U)) {
        throw std::runtime_error(
            std::format("Could not read the energy following \"{}\" in {}",
                        kEnergyMarker, kOutputFile));
      }
      *U = *U * kHartreeToEv; // Energy in hartree to eV
      haveEnergy = true;
    }
 
    if (line == kGradientMarker) { // Finding the forces
      double index;
      std::string symbol;
      for (long i = 0; i < N; i++) {
        if (!(in >> index >> symbol >> F[i * 3 + 0] >> F[i * 3 + 1] >>
              F[i * 3 + 2])) {
          throw std::runtime_error(
              std::format("{} holds gradients for {} atoms, expected {}",
                          kOutputFile, i, N));
        }
        // AMS_IO gives gradients, not forces, hence the change.
        F[i * 3 + 0] = -F[i * 3 + 0];
        F[i * 3 + 1] = -F[i * 3 + 1];
        F[i * 3 + 2] = -F[i * 3 + 2];
      }
      haveGradients = true;
    }
  }
 
  if (!haveEnergy || !haveGradients) {
    throw std::runtime_error(std::format(
        "{} holds no {}", kOutputFile,
        !haveEnergy
            ? (!haveGradients ? "energy and no gradient block" : "energy")
            : "gradient block"));
  }
 
  for (long i = 0; i < 3 * N; i++) {
    F[i] = F[i] * kHartreeBohrToEvAngstrom; // Forces from hartree/bohr to
                                            // eV/Angstrom
  }
  return;
}

Member Data Documentation

engine

std::string AMS_IO::engine

private

Definition at line 35 of file AMS_IO.h.

forcefield

std::string AMS_IO::forcefield

private

Definition at line 37 of file AMS_IO.h.

model

std::string AMS_IO::model

private

Definition at line 36 of file AMS_IO.h.

xc

std::string AMS_IO::xc

private

Definition at line 38 of file AMS_IO.h.

---

The documentation for this class was generated from the following files:

• /home/runner/work/eOn/eOn/include/eon/potentials/AMS_IO/AMS_IO.h
• /home/runner/work/eOn/eOn/client/potentials/AMS_IO/AMS_IO.cpp