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Merged
dyzheng merged 1 commit into from
Dec 3, 2021
Merged

< fix > modify freedom calculation to fix issue #497 #519

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2 changes: 1 addition & 1 deletion source/module_md/MD_basic.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ MD_basic::MD_basic(MD_parameters& MD_para_in, UnitCell_pseudo &unit_in):
allmass=new double[ucell.nat];
ionmbl=new ModuleBase::Vector3<int>[ucell.nat];

frozen_freedom_ = mdf.getMassMbl(ucell, mdp, allmass, ionmbl);
//frozen_freedom_ = mdf.getMassMbl(ucell, mdp, allmass, ionmbl);
mdf.InitVel(ucell, temperature_, allmass, frozen_freedom_, ionmbl, vel);
// if (ucell.set_vel) // Yuanbo Li 2021-08-01
// {
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36 changes: 17 additions & 19 deletions source/module_md/MD_func.cpp
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Expand Up @@ -135,6 +135,7 @@ void MD_func::RandomVel(
const int& numIon,
const double& temperature,
const double* allmass,
const ModuleBase::Vector3<int> frozen,
const int& frozen_freedom,
const ModuleBase::Vector3<int>* ionmbl,
ModuleBase::Vector3<double>* vel)
Expand Down Expand Up @@ -184,9 +185,9 @@ void MD_func::RandomVel(

for(int i=0; i<numIon; i++)
{
if(ionmbl[i].x) vel[i].x -= average.x;
if(ionmbl[i].y) vel[i].y -= average.y;
if(ionmbl[i].z) vel[i].z -= average.z;
if(ionmbl[i].x && frozen.x==0) vel[i].x -= average.x;
if(ionmbl[i].y && frozen.y==0) vel[i].y -= average.y;
if(ionmbl[i].z && frozen.z==0) vel[i].z -= average.z;
}

double factor = 0.5*(3*numIon-frozen_freedom)*temperature/GetAtomKE(numIon, vel, allmass);
Expand All @@ -210,15 +211,20 @@ void MD_func::InitVel(
ModuleBase::Vector3<int>* ionmbl,
ModuleBase::Vector3<double>* vel)
{
//frozen_freedom = getMassMbl(unit_in, allmass, ionmbl);
ModuleBase::Vector3<int> frozen;
getMassMbl(unit_in, allmass, frozen, ionmbl);
frozen_freedom = frozen.x + frozen.y + frozen.z;
if(frozen.x == 0) ++frozen_freedom;
if(frozen.y == 0) ++frozen_freedom;
if(frozen.z == 0) ++frozen_freedom;

if(unit_in.set_vel)
{
ReadVel(unit_in, vel);
}
else
{
RandomVel(unit_in.nat, temperature, allmass, frozen_freedom, ionmbl, vel);
RandomVel(unit_in.nat, temperature, allmass, frozen, frozen_freedom, ionmbl, vel);
}
}

Expand Down Expand Up @@ -357,34 +363,26 @@ std::string MD_func::intTurnTostring(long int iter, std::string path)
return path;
}

int MD_func::getMassMbl(const UnitCell_pseudo &unit_in,
const MD_parameters &mdp,
void MD_func::getMassMbl(const UnitCell_pseudo &unit_in,
double* allmass,
ModuleBase::Vector3<int> &frozen,
ModuleBase::Vector3<int>* ionmbl)
{
//some prepared information
//mass and degree of freedom
int ion=0;
int frozen_freedom=0;
frozen.set(0,0,0);
for(int it=0;it<unit_in.ntype;it++){
for(int i=0;i<unit_in.atoms[it].na;i++){
allmass[ion]=unit_in.atoms[it].mass/ModuleBase::AU_to_MASS;
ionmbl[ion]=unit_in.atoms[it].mbl[i];
if (ionmbl[ion].x==0) frozen_freedom++;
if (ionmbl[ion].y==0) frozen_freedom++;
if (ionmbl[ion].z==0) frozen_freedom++;
if (ionmbl[ion].x==0) ++frozen.x;
if (ionmbl[ion].y==0) ++frozen.y;
if (ionmbl[ion].z==0) ++frozen.z;

ion++;
}
}

// the center of mass is fixed except for NVT Anderson
if(!(mdp.mdtype==1 && mdp.NVT_control==3))
{
frozen_freedom += 3;
}

return frozen_freedom;
}

void MD_func::printpos(const std::string& file, const int& iter, const int& recordFreq, const UnitCell_pseudo& unit_in)
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5 changes: 3 additions & 2 deletions source/module_md/MD_func.h
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Expand Up @@ -37,15 +37,16 @@ class MD_func
const int& numIon,
const double& temperature,
const double* allmass,
const ModuleBase::Vector3<int> frozen,
const int& frozen_freedom,
const ModuleBase::Vector3<int>* ionmbl,
ModuleBase::Vector3<double>* vel);

// void ReadNewTemp(int step);
std::string intTurnTostring(long int iter,std::string path);
int getMassMbl(const UnitCell_pseudo &unit_in,
const MD_parameters &mdp,
void getMassMbl(const UnitCell_pseudo &unit_in,
double* allmass,
ModuleBase::Vector3<int> &frozen,
ModuleBase::Vector3<int>* ionmbl);
void printpos(const std::string& file, const int& iter, const int& recordFreq, const UnitCell_pseudo& unit_in);
void scalevel(
Expand Down