abacus-develop/source/source_md/md_base.cpp at develop · AroundPeking/abacus-develop · GitHub

History

256 lines (203 loc) · 6.51 KB

Raw

100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

143

144

145

146

147

148

149

150

151

152

153

154

155

156

157

158

159

160

161

162

163

164

165

166

167

168

169

170

171

172

173

174

175

176

177

178

179

180

181

182

183

184

185

186

187

188

189

190

191

192

193

194

195

196

197

198

199

200

201

202

203

204

205

206

207

208

209

210

211

212

213

214

215

216

217

218

219

220

221

222

223

224

225

226

227

228

229

230

231

232

233

234

235

236

237

238

239

240

241

242

243

244

245

246

247

248

249

250

251

252

253

254

255

256

#include "md_base.h"

#include "md_func.h"

#ifdef __MPI

#include "mpi.h"

#endif

#include "source_io/module_output/print_info.h"

#include "source_cell/update_cell.h"

MD_base::MD_base(const Parameter& param_in, UnitCell& unit_in)

: mdp(param_in.mdp), ucell(unit_in)

{

my_rank = param_in.globalv.myrank;

cal_stress = param_in.inp.cal_stress;

if (mdp.md_seed >= 0)

{

srand(mdp.md_seed);

}

stop = false;

assert(ucell.nat>0);

allmass = new double[ucell.nat];

pos = new ModuleBase::Vector3<double>[ucell.nat];

vel = new ModuleBase::Vector3<double>[ucell.nat];

ionmbl = new ModuleBase::Vector3<int>[ucell.nat];

force = new ModuleBase::Vector3<double>[ucell.nat];

virial.create(3, 3);

stress.create(3, 3);

assert(ModuleBase::AU_to_FS!=0.0);

assert(ModuleBase::Hartree_to_K!=0.0);

/// convert to a.u. unit

md_dt = mdp.md_dt / ModuleBase::AU_to_FS;

md_tfirst = mdp.md_tfirst / ModuleBase::Hartree_to_K;

md_tlast = mdp.md_tlast / ModuleBase::Hartree_to_K;

step_ = 0;

step_rst_ = 0;

MD_func::init_vel(ucell, my_rank, mdp.md_restart, md_tfirst, allmass, frozen_freedom_, ionmbl, vel);

t_current = MD_func::current_temp(kinetic, ucell.nat, frozen_freedom_, allmass, vel);

}

MD_base::~MD_base()

{

delete[] allmass;

delete[] pos;

delete[] vel;

delete[] ionmbl;

delete[] force;

}

void MD_base::setup(ModuleESolver::ESolver* p_esolver, const std::string& global_readin_dir)

{

if (mdp.md_restart)

{

restart(global_readin_dir);

}

// mohan add 2026-01-04

const int stress_step = 0;

const int force_step = 0;

const int istep_print = step_ + step_rst_ + 1;

ModuleIO::print_screen(stress_step, force_step, istep_print);

MD_func::force_virial(p_esolver, step_, ucell, potential, force, cal_stress, virial);

MD_func::compute_stress(ucell, vel, allmass, cal_stress, virial, stress);

ucell.ionic_position_updated = true;

return;

}

void MD_base::first_half(std::ofstream& ofs)

{

update_vel(force);

update_pos();

return;

}

void MD_base::second_half()

{

update_vel(force);

return;

}

void MD_base::update_pos()

{

if (my_rank == 0)

{

for (int i = 0; i < ucell.nat; ++i)

{

for (int k = 0; k < 3; ++k)

{

if (ionmbl[i][k])

{

pos[i][k] = vel[i][k] * md_dt / ucell.lat0;

}

else

{

pos[i][k] = 0;

}

pos[i] = pos[i] * ucell.GT;

}

#ifdef __MPI

MPI_Bcast(pos, ucell.nat * 3, MPI_DOUBLE, 0, MPI_COMM_WORLD);

#endif

unitcell::update_pos_taud(ucell.lat,pos,ucell.ntype,ucell.nat,ucell.atoms);

return;

}

void MD_base::update_vel(const ModuleBase::Vector3<double>* force)

{

if (my_rank == 0)

{

for (int i = 0; i < ucell.nat; ++i)

{

for (int k = 0; k < 3; ++k)

{

if (ionmbl[i][k])

{

vel[i][k] += 0.5 * force[i][k] * md_dt / allmass[i];

}

#ifdef __MPI

MPI_Bcast(vel, ucell.nat * 3, MPI_DOUBLE, 0, MPI_COMM_WORLD);

#endif

return;

}

void MD_base::print_md(std::ofstream& ofs, const bool& cal_stress)

{

if (my_rank!=0)

{

return;

}

t_current = MD_func::current_temp(kinetic, ucell.nat, frozen_freedom_, allmass, vel);

assert(ModuleBase::BOHR_RADIUS_SI>0.0);

const double unit_transform = ModuleBase::HARTREE_SI / pow(ModuleBase::BOHR_RADIUS_SI, 3) * 1.0e-8;

double press = 0.0;

for (int i = 0; i < 3; i++)

{

press += stress(i, i) / 3;

}

// screen output

std::cout << std::setprecision(8);

std::cout << " ------------------------------------------------------------------------------------------------"

<< std::endl;

std::cout << " " << std::left << std::setw(20) << "Energy (Ry)" << std::left << std::setw(20) << "Potential (Ry)"

<< std::left << std::setw(20) << "Kinetic (Ry)" << std::left << std::setw(20) << "Temperature (K)";

if (cal_stress)

{

std::cout << std::left << std::setw(20) << "Pressure (kbar)";

}

std::cout << std::endl;

std::cout << " " << std::left << std::setw(20) << 2 * (potential + kinetic) << std::left << std::setw(20)

<< 2 * potential << std::left << std::setw(20) << 2 * kinetic << std::left << std::setw(20)

<< t_current * ModuleBase::Hartree_to_K;

if (cal_stress)

{

std::cout << std::left << std::setw(20) << press * unit_transform;

}

std::cout << std::endl;

std::cout << " ------------------------------------------------------------------------------------------------"

<< std::endl;

// running_log output

ofs.unsetf(std::ios::fixed);

ofs << std::setprecision(8);

if (cal_stress)

{

MD_func::print_stress(ofs, virial, stress);

ofs << std::endl;

}

ofs << " ------------------------------------------------------------------------------------------------"

<< std::endl;

ofs << " " << std::left << std::setw(20) << "Energy (Ry)" << std::left << std::setw(20) << "Potential (Ry)"

<< std::left << std::setw(20) << "Kinetic (Ry)" << std::left << std::setw(20) << "Temperature (K)";

if (cal_stress)

{

ofs << std::left << std::setw(20) << "Pressure (kbar)";

}

ofs << std::endl;

ofs << " " << std::left << std::setw(20) << 2 * (potential + kinetic) << std::left << std::setw(20) << 2 * potential

<< std::left << std::setw(20) << 2 * kinetic << std::left << std::setw(20)

<< t_current * ModuleBase::Hartree_to_K;

if (cal_stress)

{

ofs << std::left << std::setw(20) << press * unit_transform;

}

ofs << std::endl;

ofs << " ------------------------------------------------------------------------------------------------"

<< std::endl;

ofs << std::endl;

return;

}

void MD_base::write_restart(const std::string& global_out_dir)

{

if (!my_rank)

{

std::stringstream ssc;

ssc << global_out_dir << "Restart_md.txt";

std::ofstream file(ssc.str().c_str());

file << step_ + step_rst_ << std::endl;

file << md_tfirst << std::endl;

file.close();

}

#ifdef __MPI

MPI_Barrier(MPI_COMM_WORLD);

#endif

return;

}

void MD_base::restart(const std::string& global_readin_dir)

{

MD_func::current_md_info(my_rank, global_readin_dir, step_rst_, md_tfirst);

return;

}

abacus-develop/source/source_md/md_base.cpp at develop · AroundPeking/abacus-develop · GitHub

Expand file tree

Breadcrumbs

md_base.cpp

Latest commit

History

Breadcrumbs

md_base.cpp

File metadata and controls