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Generalize the classes to use complex or real numbers #21

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Generalize the classes to use complex or real numbers #21

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cb73e0d
Fixed compilation error with double mode
PabloIbannez Jun 23, 2023
488beb4
Generalize the classes to use complex or real numbers (done by Pablo …
PabloIbannez Jun 23, 2023
a1aac39
Merge branch 'RaulPPelaez:v2.x' into v2.x
PabloIbannez Jul 11, 2023
64e82c5
Merge branch 'RaulPPelaez:v2.x' into v2.x
PabloIbannez Sep 13, 2023
3b838c2
Define explicitly atomic add of float2 numbers and double2 numbers
PabloPalaciosAlonso Dec 1, 2023
b2b96da
Merge pull request #1 from PabloPalaciosAlonso/v2.x
PabloIbannez Dec 4, 2023
29eb8a5
Merge branch 'RaulPPelaez:v2.x' into v2.x
PabloIbannez Dec 25, 2023
afabc46
Add transpose to tensor3
PabloIbannez Dec 25, 2023
ede066f
Added qualifiers
PabloIbannez Dec 25, 2023
e93acdf
Fixed transpose qualifier
PabloIbannez Jan 9, 2024
9d8647d
Added unary minus operator
PabloIbannez Jan 17, 2024
8724330
Merge branch 'RaulPPelaez:v2.x' into v2.x
PabloIbannez Feb 19, 2024
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4 changes: 2 additions & 2 deletions src/Integrator/BDHI/BDHI_Cholesky.cu
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Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,7 @@ namespace uammd{
//Curand fill with gaussian numbers with mean 0 and var 1
/*This shit is obscure, curand will only work with an even number of elements*/
auto d_noise = thrust::raw_pointer_cast(noise.data());
curandGenerateNormal(curng, d_noise, 3*numberParticles + ((3*numberParticles)%2), real(0.0), real(1.0));
curandgeneratenormal(curng, d_noise, 3*numberParticles + ((3*numberParticles)%2), real(0.0), real(1.0));
isMup2date = false;
}

Expand Down Expand Up @@ -219,7 +219,7 @@ namespace uammd{
3*numberParticles, d_M, 3*numberParticles, d_work, h_work_size, d_info));
curandSetStream(curng, st);
/*Gen new noise in BdW*/
curandGenerateNormal(curng,
curandgeneratenormal(curng,
(real*) BdW,
3*numberParticles + ((3*numberParticles)%2),
real(0.0), real(1.0));
Expand Down
6 changes: 3 additions & 3 deletions src/Integrator/BDHI/BDHI_Lanczos.cu
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Expand Up @@ -49,8 +49,8 @@ namespace uammd{
thrust::device_vector<real> noise(30000);
auto noise_ptr = thrust::raw_pointer_cast(noise.data());
//Warm cuRNG
curandGenerateNormal(curng, noise_ptr, noise.size(), 0.0, 1.0);
curandGenerateNormal(curng, noise_ptr, noise.size(), 0.0, 1.0);
curandgeneratenormal(curng, noise_ptr, noise.size(), 0.0, 1.0);
curandgeneratenormal(curng, noise_ptr, noise.size(), 0.0, 1.0);
}

namespace Lanczos_ns{
Expand Down Expand Up @@ -172,7 +172,7 @@ namespace uammd{
Lanczos_ns::Dotctor<real3> Mdot(rpy, this->hydrodynamicRadius, radius_ptr, nbody, st);
//Filling V instead of an external array (for v in sqrt(M)·v) is faster
uninitialized_cached_vector<real3> noise(numberParticles);
curandGenerateNormal(curng, (real*)noise.data().get(),
curandgeneratenormal(curng, (real*)noise.data().get(),
3*numberParticles + (3*numberParticles)%2,
real(0.0), real(1.0));
//lanczosAlgorithm->solve(Mdot, (real*) BdW, noise, numberParticles, st);
Expand Down
2 changes: 1 addition & 1 deletion src/Integrator/BDHI/DoublyPeriodic/DPStokesSlab.cuh
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Expand Up @@ -169,7 +169,7 @@ else throw std::runtime_error("[DPStokesSlab] Can only average in direction X (0
real gw;
real tolerance;
WallMode mode;
shared_ptr<BVP::BatchedBVPHandler> bvpSolver;
shared_ptr<BVP::BatchedBVPHandler<real>> bvpSolver;

};

Expand Down
2 changes: 1 addition & 1 deletion src/Integrator/BDHI/DoublyPeriodic/StokesSlab/Correction.cuh
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Expand Up @@ -506,7 +506,7 @@ namespace uammd{
}

auto computeZeroModeBoundaryConditions(int nz, real H, WallMode mode){
BVP::SchurBoundaryCondition bcs(nz, H);
BVP::SchurBoundaryCondition<real> bcs(nz, H);
if(mode == WallMode::bottom){
correction_ns::TopBoundaryConditions top(0, H);
correction_ns::BottomBoundaryConditions bot(0, H);
Expand Down
2 changes: 1 addition & 1 deletion src/Integrator/BDHI/DoublyPeriodic/StokesSlab/initialization.cu
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Expand Up @@ -144,7 +144,7 @@ namespace uammd{
auto botBC = thrust::make_transform_iterator(thrust::make_counting_iterator<int>(0), botdispatch);
int numberSystems = (nk.x/2+1)*nk.y;
int nz = grid.cellDim.z;
this->bvpSolver = std::make_shared<BVP::BatchedBVPHandler>(klist, topBC, botBC, numberSystems, halfH, nz);
this->bvpSolver = std::make_shared<BVP::BatchedBVPHandler<real>>(klist, topBC, botBC, numberSystems, halfH, nz);
CudaCheckError();
}

Expand Down
10 changes: 5 additions & 5 deletions src/Integrator/BDHI/FIB/FIB.cu
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Expand Up @@ -129,8 +129,8 @@ namespace uammd{
thrust::device_vector<real> noise(30000);
auto noise_ptr = thrust::raw_pointer_cast(noise.data());
//Warm cuRNG
CurandSafeCall(curandGenerateNormal(curng, noise_ptr, noise.size(), 0.0, 1.0));
CurandSafeCall(curandGenerateNormal(curng, noise_ptr, noise.size(), 0.0, 1.0));
CurandSafeCall(curandgeneratenormal(curng, noise_ptr, noise.size(), 0.0, 1.0));
CurandSafeCall(curandgeneratenormal(curng, noise_ptr, noise.size(), 0.0, 1.0));
}
catch(thrust::system_error &e){
sys->log<System::CRITICAL>("[BDHI::FIB] Thrust could not allocate necessary arrays at initialization with error: %s", e.what());
Expand Down Expand Up @@ -871,7 +871,7 @@ namespace uammd{
sys->log<System::DEBUG2>("[BDHI::FIB] Random advection");
if(temperature!=real(0.0)){
sys->log<System::DEBUG2>("[BDHI::FIB] Generate random numbers");
CurandSafeCall(curandGenerateNormal(curng,
CurandSafeCall(curandgeneratenormal(curng,
thrust::raw_pointer_cast(random.data()),
random.size(),
0.0, 1.0));
Expand Down Expand Up @@ -906,7 +906,7 @@ namespace uammd{
sys->log<System::DEBUG2>("[BDHI::FIB] Random advection");
if(temperature!=real(0.0)){
sys->log<System::DEBUG2>("[BDHI::FIB] Generate random numbers");
CurandSafeCall(curandGenerateNormal(curng,
CurandSafeCall(curandgeneratenormal(curng,
thrust::raw_pointer_cast(random.data()),
random.size(),
0.0, 1.0));
Expand All @@ -932,7 +932,7 @@ namespace uammd{
double dV = grid.cellSize.x*grid.cellSize.y*grid.cellSize.z;
real noisePrefactor = sqrt(viscosity*temperature/(dt*dV));
if(temperature!=real(0.0))
CurandSafeCall(curandGenerateNormal(curng,
CurandSafeCall(curandgeneratenormal(curng,
thrust::raw_pointer_cast(random.data()),
random.size(),
0.0, 1.0));
Expand Down
6 changes: 3 additions & 3 deletions src/Integrator/Hydro/ICM.cu
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Expand Up @@ -935,8 +935,8 @@ namespace uammd{
thrust::device_vector<real> noise(30000);
auto noise_ptr = thrust::raw_pointer_cast(noise.data());
//Warm cuRNG
CurandSafeCall(curandGenerateNormal(curng, noise_ptr, noise.size(), 0.0, 1.0));
CurandSafeCall(curandGenerateNormal(curng, noise_ptr, noise.size(), 0.0, 1.0));
CurandSafeCall(curandgeneratenormal(curng, noise_ptr, noise.size(), 0.0, 1.0));
CurandSafeCall(curandgeneratenormal(curng, noise_ptr, noise.size(), 0.0, 1.0));
}
//Sum S·F term using the current particle positions
void ICM::spreadParticleForces(){
Expand Down Expand Up @@ -993,7 +993,7 @@ namespace uammd{
if(temperature!=real(0.0)){
CurandSafeCall(curandSetStream(curng, st));
sys->log<System::DEBUG2>("[Hydro::ICM] Generate random numbers");
CurandSafeCall(curandGenerateNormal(curng, thrust::raw_pointer_cast(random.data()), random.size(), 0.0, 1.0));
CurandSafeCall(curandgeneratenormal(curng, thrust::raw_pointer_cast(random.data()), random.size(), 0.0, 1.0));
}
real3* d_gridVels = (real3*)thrust::raw_pointer_cast(gridVels.data());
real3* d_cellAdvection = (real3*)thrust::raw_pointer_cast(cellAdvection.data());
Expand Down
5 changes: 0 additions & 5 deletions src/Integrator/VerletNVE.cu
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Expand Up @@ -28,11 +28,6 @@

#include"VerletNVE.cuh"


#ifndef SINGLE_PRECISION
#define curandGenerateNormal curandGenerateNormalDouble
#endif

namespace uammd{

VerletNVE::VerletNVE(shared_ptr<ParticleGroup> pg, VerletNVE::Parameters par):
Expand Down
4 changes: 2 additions & 2 deletions src/Interactor/DoublyPeriodic/PoissonSlab/BVPPoisson.cuh
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Expand Up @@ -90,7 +90,7 @@ namespace uammd{
}

class BVPPoissonSlab{
std::shared_ptr<BVP::BatchedBVPHandler> bvpSolver;
std::shared_ptr<BVP::BatchedBVPHandler<real>> bvpSolver;
real2 Lxy;
real H;
int3 cellDim;
Expand Down Expand Up @@ -150,7 +150,7 @@ namespace uammd{
BoundaryConditionsDispatch<BottomBoundaryConditions, decltype(klist)>(klist, H));

int numberSystems = (nk.x/2+1)*nk.y;
this->bvpSolver = std::make_shared<BVP::BatchedBVPHandler>(klist, topBC, bottomBC, numberSystems, H, cellDim.z);
this->bvpSolver = std::make_shared<BVP::BatchedBVPHandler<real>>(klist, topBC, bottomBC, numberSystems, H, cellDim.z);
CudaCheckError();
}
};
Expand Down
25 changes: 14 additions & 11 deletions src/misc/BoundaryValueProblem/BVPSchurComplementMatrices.cuh
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Expand Up @@ -117,6 +117,7 @@ namespace uammd{
}
};

template <typename T>
class SchurBoundaryCondition{
int nz;
real H;
Expand All @@ -125,8 +126,8 @@ namespace uammd{
SchurBoundaryCondition(int nz, real H):nz(nz), H(H), bcs(nz){}

template<class TopBC, class BottomBC>
std::vector<real> computeBoundaryConditionMatrix(const TopBC &top, const BottomBC &bottom){
std::vector<real> CandD(2*nz+4, 0);
std::vector<T> computeBoundaryConditionMatrix(const TopBC &top, const BottomBC &bottom){
std::vector<T> CandD(2*nz+4, 0);
auto topRow = computeTopRow(top, bottom);
auto bottomRow = computeBottomRow(top, bottom);
std::copy(topRow.begin(), topRow.end()-2, CandD.begin());
Expand All @@ -141,8 +142,8 @@ namespace uammd{
private:

template<class TopBC, class BottomBC>
std::vector<real> computeTopRow(const TopBC &top, const BottomBC &bottom){
std::vector<real> topRow(nz+2, 0);
std::vector<T> computeTopRow(const TopBC &top, const BottomBC &bottom){
std::vector<T> topRow(nz+2, 0);
auto tfi = bcs.topFirstIntegral();
auto tsi = bcs.topSecondIntegral();
auto tfiFactor = top.getFirstIntegralFactor();
Expand All @@ -156,8 +157,8 @@ namespace uammd{
}

template<class TopBC, class BottomBC>
std::vector<real> computeBottomRow(const TopBC &top, const BottomBC &bottom){
std::vector<real> bottomRow(nz+2, 0);
std::vector<T> computeBottomRow(const TopBC &top, const BottomBC &bottom){
std::vector<T> bottomRow(nz+2, 0);
auto bfi = bcs.bottomFirstIntegral();
auto bsi = bcs.bottomSecondIntegral();
auto bfiFactor = bottom.getFirstIntegralFactor();
Expand All @@ -172,10 +173,11 @@ namespace uammd{

};

std::vector<real> computeSecondIntegralMatrix(real k, real H, int nz){
std::vector<real> A(nz*nz, 0);
template<class T>
std::vector<T> computeSecondIntegralMatrix(T k, real H, int nz){
std::vector<T> A(nz*nz, 0);
SecondIntegralMatrix sim(nz);
real kH2 = k*k*H*H;
T kH2 = k*k*H*H;
fori(0, nz){
forj(0,nz){
A[i+nz*j] = (i==j) - kH2*sim.getElement(i, j);
Expand All @@ -184,9 +186,10 @@ namespace uammd{
return std::move(A);
}

std::vector<real> computeInverseSecondIntegralMatrix(real k, real H, int nz){
template<class T>
std::vector<T> computeInverseSecondIntegralMatrix(T k, real H, int nz){
if(k==0){
std::vector<real> invA(nz*nz, 0);
std::vector<T> invA(nz*nz, 0);
fori(0, nz){
invA[i+nz*i] = 1;
}
Expand Down