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Merge pull request #61 from Zhaoli2042/main
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PR: small change of code and initial pybind mix
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@Xiaoyi-ZHANG23
Xiaoyi-ZHANG23 authored Jan 27, 2025
2 parents 2b9c6e9 + f8b22f7 commit 8ae6d74
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19 changes: 12 additions & 7 deletions README.md
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Expand Up @@ -28,6 +28,11 @@ A detailed installation note for gRASPA on CentOS/Ubuntu 24.04 is documented in
* A40, A100, RTX 3080 Ti, RTX 3090, RTX 4090.
* 🤯: RTX 3090/4090 is faster than A40/A100 for gRASPA
* gRASPA has a SYCL version (experimental) that supports other devices, available in [Releases](https://github.com/snurr-group/gRASPA/releases)

### Pybind Extension (testing)
* Pybind extension for gRASPA allows user to interact with the **internal variables** of gRASPA, break down **MC moves**, add their **modifications**
* Access the pybind-gRASPA extension [here](https://github.com/Zhaoli2042/gRASPA_pybind), as a patch to the original code

## Quick Start
* Go to [```Examples/```](Examples/) folder and read more!

Expand Down Expand Up @@ -75,11 +80,11 @@ A detailed installation note for gRASPA on CentOS/Ubuntu 24.04 is documented in
| Automatic Determination<br>of # unit cells | | | :heavy_check_mark: |

## Authors
* Zhao Li (Northwestern University, currently at Purdue University)
* Kaihang Shi (Northwestern University, currently at University at Buffalo)
* David Dubbeldam (University of Amsterdam)
* Mark Dewing (Argonne National Laboratory)
* Christopher Knight (Argonne National Laboratory)
* Alvaro Vazquez Mayagoitia (Argonne National Laboratory)
* Randall Q. Snurr (Northwestern University)
* Zhao Li (Northwestern University, currently at Purdue University/University of Notre Dame, [email protected])
* Kaihang Shi (Northwestern University, currently at University at Buffalo, [email protected])
* David Dubbeldam (University of Amsterdam, [email protected])
* Mark Dewing (Argonne National Laboratory, [email protected])
* Christopher Knight (Argonne National Laboratory, [email protected])
* Alvaro Vazquez Mayagoitia (Argonne National Laboratory, [email protected])
* Randall Q. Snurr (Northwestern University, [email protected])

24 changes: 19 additions & 5 deletions src_clean/DNN_HostGuest_Energy_Functions.h
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Expand Up @@ -10,8 +10,15 @@
#include "read_data.h"
//###PATCH_LCLIN_INCLUDE_HEADER###//

__global__ void Initialize_DNN_Positions(Atoms* d_a, Atoms New, Atoms Old, size_t Oldsize, size_t Newsize, size_t SelectedComponent, size_t Location, size_t chainsize, int MoveType, size_t CYCLE)
__global__ void Initialize_DNN_Positions(Atoms* d_a, Atoms New, Atoms Old, double3* temp, size_t Oldsize, size_t Newsize, size_t SelectedComponent, size_t Location, size_t chainsize, int MoveType, size_t CYCLE)
{
size_t ij = blockIdx.x * blockDim.x + threadIdx.x;

if(ij < (Newsize + Oldsize))
{
Initialize_Copy_Positions_Together(d_a, New, Old, temp, Oldsize, Newsize, SelectedComponent, Location, chainsize, MoveType);
}
/*
//Zhao's note: need to think about changing this boolean to switch//
if(MoveType == TRANSLATION || MoveType == ROTATION || MoveType == SINGLE_INSERTION || MoveType == SINGLE_DELETION) // Translation/Rotation/single_insertion/single_deletion //
{
Expand Down Expand Up @@ -53,6 +60,8 @@ __global__ void Initialize_DNN_Positions(Atoms* d_a, Atoms New, Atoms Old, size_
Old.scaleCoul[i] = d_a[SelectedComponent].scaleCoul[Location + i];
}
}
*/

/*
if(CYCLE == 145)
{
Expand All @@ -62,7 +71,7 @@ __global__ void Initialize_DNN_Positions(Atoms* d_a, Atoms New, Atoms Old, size_
*/
}

void Prepare_DNN_InitialPositions(Atoms*& d_a, Atoms& New, Atoms& Old, Components& SystemComponents, size_t SelectedComponent, int MoveType, size_t Location)
void Prepare_DNN_InitialPositions(Atoms*& d_a, Atoms& New, Atoms& Old, double3* temp, Components& SystemComponents, size_t SelectedComponent, int MoveType, size_t Location)
{
size_t Oldsize = 0; size_t Newsize = 0; size_t chainsize = 0;
switch(MoveType)
Expand Down Expand Up @@ -90,8 +99,11 @@ void Prepare_DNN_InitialPositions(Atoms*& d_a, Atoms& New, Atoms& Old, Component
}
case REINSERTION: // Reinsertion //
{
throw std::runtime_error("Use the Special Function for Reinsertion");
//break;
Oldsize = SystemComponents.Moleculesize[SelectedComponent];
Newsize = SystemComponents.Moleculesize[SelectedComponent];
chainsize = SystemComponents.Moleculesize[SelectedComponent];
//throw std::runtime_error("Use the Special Function for Reinsertion");
break;
}
case IDENTITY_SWAP:
{
Expand Down Expand Up @@ -120,7 +132,9 @@ void Prepare_DNN_InitialPositions(Atoms*& d_a, Atoms& New, Atoms& Old, Component
break;
}
}
Initialize_DNN_Positions<<<1,1>>>(d_a, New, Old, Oldsize, Newsize, SelectedComponent, Location, chainsize, MoveType, SystemComponents.CURRENTCYCLE);
//Initialize_DNN_Positions<<<1,1>>>(d_a, New, Old, Oldsize, Newsize, SelectedComponent, Location, chainsize, MoveType, SystemComponents.CURRENTCYCLE);
size_t Nblock = 0; size_t Nthread = 0; Setup_threadblock(Oldsize + Newsize, Nblock, Nthread);
Initialize_DNN_Positions<<<Nblock,Nthread>>>(d_a, New, Old, SystemComponents.tempMolStorage, Oldsize, Newsize, SelectedComponent, Location, chainsize, MoveType, SystemComponents.CURRENTCYCLE);
}

__global__ void Initialize_DNN_Positions_Reinsertion(double3* temp, Atoms* d_a, Atoms Old, size_t Oldsize, size_t Newsize, size_t realpos, size_t SelectedComponent)
Expand Down
130 changes: 61 additions & 69 deletions src_clean/Ewald_Energy_Functions.h
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Expand Up @@ -102,46 +102,71 @@ __device__ void Initialize_Vectors_thread(Complex* eik, size_t numberOfAtoms, in
eik[i + k * numberOfAtoms] = multiply(eik[i + (k - 1) * numberOfAtoms], eik[i + 1 * numberOfAtoms]);
}
}

__global__ void Initialize_WaveVector_General(Boxsize Box, int3 kmax, Atoms* d_a, Atoms New, Atoms Old, size_t Oldsize, size_t Newsize, size_t SelectedComponent, size_t Location, size_t chainsize, size_t numberOfAtoms, int MoveType)
//Copy Old positions and new positions together into Old//
//including double3* temp, for reinsertion//
__device__ void Initialize_Copy_Positions_Together(Atoms*& d_a, Atoms& New, Atoms& Old, double3* temp, size_t Oldsize, size_t Newsize, size_t SelectedComponent, size_t Location, size_t chainsize, int MoveType)
{
//Zhao's note: need to think about changing this boolean to switch//
size_t ij = blockIdx.x * blockDim.x + threadIdx.x;
if(ij < (Newsize + Oldsize))
if(MoveType == TRANSLATION || MoveType == ROTATION || MoveType == SPECIAL_ROTATION || MoveType == SINGLE_INSERTION || MoveType == SINGLE_DELETION) // Translation/Rotation/single_insertion/single_deletion //
{
if(MoveType == TRANSLATION || MoveType == ROTATION || MoveType == SPECIAL_ROTATION || MoveType == SINGLE_INSERTION || MoveType == SINGLE_DELETION) // Translation/Rotation/single_insertion/single_deletion //
//For Translation/Rotation, the Old positions are already in the Old struct, just need to put the New positions into Old, after the Old positions//
if(ij >= Oldsize)
{
//For Translation/Rotation, the Old positions are already in the Old struct, just need to put the New positions into Old, after the Old positions//
if(ij >= Oldsize)
{
Old.pos[ij] = New.pos[ij - Oldsize];
Old.scale[ij] = New.scale[ij - Oldsize];
Old.charge[ij] = New.charge[ij - Oldsize];
Old.scaleCoul[ij] = New.scaleCoul[ij - Oldsize];
}
Old.pos[ij] = New.pos[ij - Oldsize];
Old.scale[ij] = New.scale[ij - Oldsize];
Old.charge[ij] = New.charge[ij - Oldsize];
Old.scaleCoul[ij] = New.scaleCoul[ij - Oldsize];
}
else if(MoveType == INSERTION || MoveType == CBCF_INSERTION) // Insertion & Fractional Insertion //
}
else if(MoveType == INSERTION || MoveType == CBCF_INSERTION) // Insertion & Fractional Insertion //
{
//Put the trial orientations in New to Old, right after the first bead position//
if(ij < chainsize)
{
//Put the trial orientations in New to Old, right after the first bead position//
if(ij < chainsize)
{
Old.pos[ij + 1] = New.pos[Location * chainsize + ij];
Old.scale[ij + 1] = New.scale[Location * chainsize + ij];
Old.charge[ij + 1] = New.charge[Location * chainsize + ij];
Old.scaleCoul[ij + 1] = New.scaleCoul[Location * chainsize + ij];
}
Old.pos[ij + 1] = New.pos[Location * chainsize + ij];
Old.scale[ij + 1] = New.scale[Location * chainsize + ij];
Old.charge[ij + 1] = New.charge[Location * chainsize + ij];
Old.scaleCoul[ij + 1] = New.scaleCoul[Location * chainsize + ij];
}
else if(MoveType == DELETION || MoveType == CBCF_DELETION) // Deletion //
}
else if(MoveType == DELETION || MoveType == CBCF_DELETION) // Deletion //
{
if(ij < Oldsize)
{
if(ij < Oldsize)
{
// For deletion, Location = UpdateLocation, see Deletion Move //
Old.pos[ij] = d_a[SelectedComponent].pos[Location + ij];
Old.scale[ij] = d_a[SelectedComponent].scale[Location + ij];
Old.charge[ij] = d_a[SelectedComponent].charge[Location + ij];
Old.scaleCoul[ij] = d_a[SelectedComponent].scaleCoul[Location + ij];
}
// For deletion, Location = UpdateLocation, see Deletion Move //
Old.pos[ij] = d_a[SelectedComponent].pos[Location + ij];
Old.scale[ij] = d_a[SelectedComponent].scale[Location + ij];
Old.charge[ij] = d_a[SelectedComponent].charge[Location + ij];
Old.scaleCoul[ij] = d_a[SelectedComponent].scaleCoul[Location + ij];
}
}
else if(MoveType == REINSERTION)
{
if(ij < Oldsize)
{
Old.pos[ij] = d_a[SelectedComponent].pos[Location + ij];
Old.scale[ij] = d_a[SelectedComponent].scale[Location + ij];
Old.charge[ij] = d_a[SelectedComponent].charge[Location + ij];
Old.scaleCoul[ij] = d_a[SelectedComponent].scaleCoul[Location + ij];
}
else
{
Old.pos[ij] = temp[ij - Oldsize];
Old.scale[ij] = d_a[SelectedComponent].scale[Location + ij - Oldsize];
Old.charge[ij] = d_a[SelectedComponent].charge[Location + ij - Oldsize];
Old.scaleCoul[ij] = d_a[SelectedComponent].scaleCoul[Location + ij - Oldsize];
}
}
}

__global__ void Initialize_WaveVector_General(Boxsize Box, int3 kmax, Atoms* d_a, Atoms New, Atoms Old, double3* temp, size_t Oldsize, size_t Newsize, size_t SelectedComponent, size_t Location, size_t chainsize, size_t numberOfAtoms, int MoveType)
{
//Zhao's note: need to think about changing this boolean to switch//
size_t ij = blockIdx.x * blockDim.x + threadIdx.x;

if(ij < (Newsize + Oldsize))
{
Initialize_Copy_Positions_Together(d_a, New, Old, temp, Oldsize, Newsize, SelectedComponent, Location, chainsize, MoveType);
//Old+New//
Complex tempcomplex; tempcomplex.real = 1.0; tempcomplex.imag = 0.0;
tempcomplex.real = 1.0; tempcomplex.imag = 0.0;
Expand Down Expand Up @@ -224,8 +249,6 @@ __global__ void Initialize_WaveVector_IdentitySwap(Boxsize Box, int3 kmax, doubl
Old.charge[ij] = d_a[NEWComponent].charge[ij - Oldsize];
Old.scaleCoul[ij] = 1.0;
}


//Old+New//
Complex tempcomplex; tempcomplex.real = 1.0; tempcomplex.imag = 0.0;
tempcomplex.real = 1.0; tempcomplex.imag = 0.0;
Expand Down Expand Up @@ -467,8 +490,10 @@ double2 GPU_EwaldDifference_General(Simulations& Sim, ForceField& FF, Components
}
case REINSERTION: // Reinsertion //
{
throw std::runtime_error("EWALD: Use the Special Function for Reinsertion");
//break;
Newsize = SystemComponents.Moleculesize[SelectedComponent];
Oldsize = SystemComponents.Moleculesize[SelectedComponent];
chainsize = SystemComponents.Moleculesize[SelectedComponent] - 1;
break;
}
case IDENTITY_SWAP:
{
Expand Down Expand Up @@ -501,7 +526,7 @@ double2 GPU_EwaldDifference_General(Simulations& Sim, ForceField& FF, Components
size_t numberOfAtoms = Oldsize + Newsize;

size_t Nblock = 0; size_t Nthread = 0; Setup_threadblock(Oldsize + Newsize, Nblock, Nthread);
Initialize_WaveVector_General<<<Nblock,Nthread>>>(Box, Box.kmax, d_a, New, Old, Oldsize, Newsize, SelectedComponent, Location, chainsize, numberOfAtoms, MoveType); checkCUDAErrorEwald("error Initializing Ewald Vectors");
Initialize_WaveVector_General<<<Nblock,Nthread>>>(Box, Box.kmax, d_a, New, Old, SystemComponents.tempMolStorage, Oldsize, Newsize, SelectedComponent, Location, chainsize, numberOfAtoms, MoveType); checkCUDAErrorEwald("error Initializing Ewald Vectors");

//Fourier Loop//
size_t numberOfStructureFactors = (Box.kmax.x + 1) * (2 * Box.kmax.y + 1) * (2 * Box.kmax.z + 1);
Expand Down Expand Up @@ -552,39 +577,6 @@ double2 GPU_EwaldDifference_General(Simulations& Sim, ForceField& FF, Components
return {SameSum, 2.0 * CrossSum};
}

//Zhao's note: THIS IS A SPECIAL FUNCTION JUST FOR REINSERTION//
double2 GPU_EwaldDifference_Reinsertion(Boxsize& Box, Atoms*& d_a, Atoms& Old, double3* temp, ForceField& FF, double* Blocksum, Components& SystemComponents, size_t SelectedComponent, size_t UpdateLocation)
{
if(FF.noCharges && !SystemComponents.hasPartialCharge[SelectedComponent]) return {0.0, 0.0};
double alpha = Box.Alpha; double alpha_squared = alpha * alpha;
double prefactor = Box.Prefactor * (2.0 * M_PI / Box.Volume);

size_t numberOfAtoms = SystemComponents.Moleculesize[SelectedComponent];
size_t Oldsize = 0; size_t Newsize = numberOfAtoms;
//Zhao's note: translation/rotation/reinsertion involves new + old states. Insertion/Deletion only has the new state.
Oldsize = SystemComponents.Moleculesize[SelectedComponent];
numberOfAtoms += Oldsize;

Complex* SameType = Box.AdsorbateEik; Complex* CrossType = Box.FrameworkEik;

// Construct exp(ik.r) for atoms and k-vectors kx, ky, kz = 0, 1 explicitly
size_t Nblock = 0; size_t Nthread = 0; Setup_threadblock(Oldsize + Newsize, Nblock, Nthread);
Initialize_WaveVector_Reinsertion<<<Nblock,Nthread>>>(Box, Box.kmax, temp, d_a, Old, Oldsize, Newsize, UpdateLocation, numberOfAtoms, SelectedComponent);

//Fourier Loop//
size_t numberOfStructureFactors = (Box.kmax.x + 1) * (2 * Box.kmax.y + 1) * (2 * Box.kmax.z + 1);
Nblock = 0; Nthread = 0; Setup_threadblock(numberOfStructureFactors, Nblock, Nthread);
Fourier_Ewald_Diff<<<Nblock * 2, Nthread, Nthread * sizeof(double)>>>(Box, SameType, CrossType, Old, alpha_squared, prefactor, Box.kmax, Oldsize, Newsize, Blocksum, false, Nblock);
//double sum[Nblock * 2];
double SameSum = 0.0; double CrossSum = 0.0;
cudaMemcpy(SystemComponents.host_array, Blocksum, 2 * Nblock * sizeof(double), cudaMemcpyDeviceToHost);

for(size_t i = 0; i < Nblock; i++){SameSum += SystemComponents.host_array[i];}
for(size_t i = Nblock; i < 2 * Nblock; i++){CrossSum += SystemComponents.host_array[i];}

return {SameSum, 2.0 * CrossSum};
}

double2 GPU_EwaldDifference_IdentitySwap(Boxsize& Box, Atoms*& d_a, Atoms& Old, double3* temp, ForceField& FF, double* Blocksum, Components& SystemComponents, size_t OLDComponent, size_t NEWComponent, size_t UpdateLocation)
{
if(FF.noCharges && !SystemComponents.hasPartialCharge[NEWComponent] && !SystemComponents.hasPartialCharge[OLDComponent]) return {0.0, 0.0};
Expand Down
4 changes: 1 addition & 3 deletions src_clean/VDW_Coulomb.cuh
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Expand Up @@ -98,8 +98,6 @@ __global__ void Energy_difference_LambdaChange(Boxsize Box, Atoms* System, Atoms
//////////////////////
double CPU_EwaldDifference(Boxsize& Box, Atoms& New, Atoms& Old, ForceField& FF, Components& SystemComponents, size_t SelectedComponent, bool Swap, size_t SelectedTrial);

double2 GPU_EwaldDifference_Reinsertion(Boxsize& Box, Atoms*& d_a, Atoms& Old, double3* temp, ForceField& FF, double* Blocksum, Components& SystemComponents, size_t SelectedComponent, size_t UpdateLocation);

double2 GPU_EwaldDifference_IdentitySwap(Boxsize& Box, Atoms*& d_a, Atoms& Old, double3* temp, ForceField& FF, double* Blocksum, Components& SystemComponents, size_t OLDComponent, size_t NEWComponent, size_t UpdateLocation);

void Copy_Ewald_Vector(Simulations& Sim);
Expand Down Expand Up @@ -149,7 +147,7 @@ double TailCorrectionIdentitySwap(Components& SystemComponents, size_t NEWCompon
// Deep Potential For Host-Guest //
// General Functions //
///////////////////////////////////
void Prepare_DNN_InitialPositions(Atoms*& d_a, Atoms& New, Atoms& Old, Components& SystemComponents, size_t SelectedComponent, int MoveType, size_t Location);
void Prepare_DNN_InitialPositions(Atoms*& d_a, Atoms& New, Atoms& Old, double3* temp, Components& SystemComponents, size_t SelectedComponent, int MoveType, size_t Location);

void Prepare_DNN_InitialPositions_Reinsertion(Atoms*& d_a, Atoms& Old, double3* temp, Components& SystemComponents, size_t SelectedComponent, size_t Location);

Expand Down
2 changes: 1 addition & 1 deletion src_clean/axpy.cu
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Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,7 @@ void Select_Box_Component_Molecule(Variables& Vars, size_t box_index)

Vars.RandomNumber = Get_Uniform_Random();
}
inline void RunMoves(Variables& Vars, size_t box_index, int Cycle)
void RunMoves(Variables& Vars, size_t box_index, int Cycle)
{
MC_MOVES MOVES;

Expand Down
17 changes: 6 additions & 11 deletions src_clean/axpy.h
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@ void Calculate_Exclusion_Energy_Rigid(Boxsize& Box, Atoms* System, ForceField FF
void Check_WaveVector_CPUGPU(Boxsize& Box, Components& SystemComponents);
*/

void RunMoves(Variables& Vars, size_t box_index, int Cycle);

double CreateMolecule_InOneBox(Variables& Vars, size_t systemId, bool AlreadyHasFractionalMolecule);

void Run_Simulation_MultipleBoxes(Variables& Vars);
Expand Down Expand Up @@ -49,7 +51,10 @@ __global__ void StoreNewLocation_Reinsertion(Atoms Mol, Atoms NewMol, double3* t
__global__ void Update_Reinsertion_data(Atoms* d_a, double3* temp, size_t SelectedComponent, size_t UpdateLocation);

double GetPrefactor(Components& SystemComponents, Simulations& Sims, size_t SelectedComponent, int MoveType);
void AcceptInsertion(Variables& Vars, size_t systemId, int MoveType, CBMC_Variables& InsertionVariables);

//void AcceptInsertion(Variables& Vars, size_t systemId, int MoveType, CBMC_Variables& InsertionVariables);
void AcceptInsertion(Variables& Vars, CBMC_Variables& InsertionVariables, size_t systemId, int MoveType);

void AcceptDeletion(Variables& Vars, size_t systemId, int MoveType);
MoveEnergy Insertion_Body(Variables& Vars, size_t systemId, CBMC_Variables& CBMC);
MoveEnergy Deletion_Body(Variables& Vars, size_t systemId, CBMC_Variables& CBMC);
Expand All @@ -72,14 +77,4 @@ struct SingleMove
}
};

//struct InsertionMove;
//struct InsertionMove {};
//struct MC_MOVES {};
/*
struct MC_MOVES
{
InsertionMove INSERTION;
};
*/

#include "move_struct.h"
1 change: 1 addition & 0 deletions src_clean/data_struct.h
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Original file line number Diff line number Diff line change
Expand Up @@ -1229,6 +1229,7 @@ struct Simulations //For multiple simulations//
Atoms* d_a; // Pointer For Atom Data in the Simulation Box //
Atoms Old; // Temporary data storage for Old Configuration //
Atoms New; // Temporary data storage for New Configuration //
Atoms Temp; // Temporary storage (for xfering data and accepting move) //
int2* ExcludeList; // Atoms to exclude during energy calculations: x: component, y: molecule-ID (may need to add z and make it int3, z: atom-ID)
double* Blocksum; // Block sums for partial reduction //
bool* device_flag; // flags for overlaps on the device //
Expand Down
5 changes: 3 additions & 2 deletions src_clean/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -272,8 +272,9 @@ Variables Initialize(void) //for pybind
Prepare_TempSystem_On_Host(Vars.SystemComponents[a].TempSystem);
cudaMemcpy(Vars.Sims[a].d_a, device_System, sizeof(Atoms)*NComponents.x, cudaMemcpyHostToDevice);
// SET UP TEMPORARY ARRAYS //
Setup_Temporary_Atoms_Structure(Vars.Sims[a].Old, Vars.SystemComponents[a].HostSystem);
Setup_Temporary_Atoms_Structure(Vars.Sims[a].New, Vars.SystemComponents[a].HostSystem);
Setup_Temporary_Atoms_Structure(Vars.Sims[a].Old, Vars.SystemComponents[a].HostSystem);
Setup_Temporary_Atoms_Structure(Vars.Sims[a].New, Vars.SystemComponents[a].HostSystem);
Setup_Temporary_Atoms_Structure(Vars.Sims[a].Temp, Vars.SystemComponents[a].HostSystem);

if(Vars.SystemComponents[a].UseDNNforHostGuest)
{
Expand Down
6 changes: 6 additions & 0 deletions src_clean/main.h
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
Variables Initialize(void);
void RunSimulation(Variables& Vars);
void EndOfSimulationWrapUp(Variables& Vars);

MoveEnergy check_energy_wrapper(Variables& Var, size_t i);
void ENERGY_SUMMARY(Variables& Vars);
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