Merge branch 'master' into user-cgdna (ed0a347f) · Commits · 郑智淋 / lammps

doc/src/Manual.txt

+2 −2

Original line number	Diff line number	Diff line
		<!-- HTML_ONLY -->
		<HEAD>
		<TITLE>LAMMPS Users Manual</TITLE>
		<META NAME="docnumber" CONTENT="20 Jan 2017 version">
		<META NAME="docnumber" CONTENT="26 Jan 2017 version">
		<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
		<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
		</HEAD>
		@@ -21,7 +21,7 @@
		<H1></H1>

		LAMMPS Documentation :c,h3
		20 Jan 2017 version :c,h4
		26 Jan 2017 version :c,h4

		Version info: :h4

potentials/WL.meam

0 → 100644

+13 −0

Original line number	Diff line number	Diff line
		# DATE: 2017-01-25 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov, CITATION: Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001)
		rc = 3.8
		delr = 0.1
		augt1 = 0
		erose_form = 2
		zbl(1,1) = 0
		nn2(1,1) = 1
		Ec(1,1) = 8.66
		re(1,1) = 2.74
		attrac(1,1) = 0
		repuls(1,1) = 0
		Cmin(1,1,1) = 0.49
		Cmax(1,1,1) = 2.8

src/KOKKOS/domain_kokkos.cpp

+8 −4

Original line number	Diff line number	Diff line
		@@ -402,7 +402,6 @@ void DomainKokkos::pbc()
		void DomainKokkos::remap_all()
		{
		atomKK->sync(Device,X_MASK \| IMAGE_MASK);
		atomKK->modified(Device,X_MASK \| IMAGE_MASK);

		x = atomKK->k_x.view<LMPDeviceType>();
		image = atomKK->k_image.view<LMPDeviceType>();
		@@ -428,6 +427,8 @@ void DomainKokkos::remap_all()
		LMPDeviceType::fence();
		copymode = 0;

		atomKK->modified(Device,X_MASK \| IMAGE_MASK);

		if (triclinic) lamda2x(nlocal);
		}

		@@ -521,7 +522,6 @@ void DomainKokkos::image_flip(int m_in, int n_in, int p_in)
		p_flip = p_in;

		atomKK->sync(Device,IMAGE_MASK);
		atomKK->modified(Device,IMAGE_MASK);

		image = atomKK->k_image.view<LMPDeviceType>();
		int nlocal = atomKK->nlocal;
		@@ -530,6 +530,8 @@ void DomainKokkos::image_flip(int m_in, int n_in, int p_in)
		Kokkos::parallel_for(Kokkos::RangePolicy<LMPDeviceType, TagDomain_image_flip>(0,nlocal),*this);
		LMPDeviceType::fence();
		copymode = 0;

		atomKK->modified(Device,IMAGE_MASK);
		}

		KOKKOS_INLINE_FUNCTION
		@@ -554,7 +556,6 @@ void DomainKokkos::operator()(TagDomain_image_flip, const int &i) const {
		void DomainKokkos::lamda2x(int n)
		{
		atomKK->sync(Device,X_MASK);
		atomKK->modified(Device,X_MASK);

		x = atomKK->k_x.view<LMPDeviceType>();

		@@ -562,6 +563,8 @@ void DomainKokkos::lamda2x(int n)
		Kokkos::parallel_for(Kokkos::RangePolicy<LMPDeviceType, TagDomain_lamda2x>(0,n),*this);
		LMPDeviceType::fence();
		copymode = 0;

		atomKK->modified(Device,X_MASK);
		}

		KOKKOS_INLINE_FUNCTION
		@@ -579,7 +582,6 @@ void DomainKokkos::operator()(TagDomain_lamda2x, const int &i) const {
		void DomainKokkos::x2lamda(int n)
		{
		atomKK->sync(Device,X_MASK);
		atomKK->modified(Device,X_MASK);

		x = atomKK->k_x.view<LMPDeviceType>();

		@@ -587,6 +589,8 @@ void DomainKokkos::x2lamda(int n)
		Kokkos::parallel_for(Kokkos::RangePolicy<LMPDeviceType, TagDomain_x2lamda>(0,n),*this);
		LMPDeviceType::fence();
		copymode = 0;

		atomKK->modified(Device,X_MASK);
		}

		KOKKOS_INLINE_FUNCTION

src/KOKKOS/fix_langevin_kokkos.cpp

+6 −3

Original line number	Diff line number	Diff line
		@@ -177,11 +177,12 @@ void FixLangevinKokkos<DeviceType>::post_force(int vflag)

		// account for bias velocity
		if(tbiasflag == BIAS){
		atomKK->sync(temperature->execution_space,temperature->datamask_read);
		temperature->compute_scalar();
		temperature->remove_bias_all(); // modifies velocities
		// if temeprature compute is kokkosized host-devcie comm won't be needed
		atomKK->modified(Host,V_MASK);
		atomKK->sync(execution_space,V_MASK);
		atomKK->modified(temperature->execution_space,temperature->datamask_modify);
		atomKK->sync(execution_space,temperature->datamask_modify);
		}

		// compute langevin force in parallel on the device
		@@ -508,8 +509,10 @@ void FixLangevinKokkos<DeviceType>::post_force(int vflag)
		DeviceType::fence();

		if(tbiasflag == BIAS){
		atomKK->sync(temperature->execution_space,temperature->datamask_read);
		temperature->restore_bias_all(); // modifies velocities
		atomKK->modified(Host,V_MASK);
		atomKK->modified(temperature->execution_space,temperature->datamask_modify);
		atomKK->sync(execution_space,temperature->datamask_modify);
		}

		// set modify flags for the views modified in post_force functor

src/KOKKOS/math_special_kokkos.h

+3 −4

Original line number	Diff line number	Diff line
		@@ -42,12 +42,11 @@ namespace MathSpecialKokkos {
		{
		x *= x;
		x *= 1.4426950408889634074; // log_2(e)
		#if defined(__BYTE_ORDER__)
		#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
		#if defined(__BYTE_ORDER__) && __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
		return (x < 1023.0) ? exp2_x86(-x) : 0.0;
		#endif
		#endif
		#else
		return (x < 1023.0) ? exp2(-x) : 0.0;
		#endif
		}

		// x**2, use instead of pow(x,2.0)

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