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remove trailing whitespace

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Axel Kohlmeyer 2020-06-30 17:48:18 -04:00
parent 1035dcd4cc
commit 6af407d01e
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14 changed files with 70 additions and 70 deletions
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10
doc/src/compute_orientorder_atom.rst
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@ -61,8 +61,8 @@ The summation is over the *nnn* nearest
neighbors of the central atom.
The angles :math:`theta` and :math:`phi` are the standard spherical polar angles
defining the direction of the bond vector :math:`r_{ij}`.
The phase and sign of :math:`Y_{lm}` follow the standard conventions,
so that :math:`{\rm sign}(Y_{ll}(0,0)) = (-1)^l`.
The phase and sign of :math:`Y_{lm}` follow the standard conventions,
so that :math:`{\rm sign}(Y_{ll}(0,0)) = (-1)^l`.
The second equation defines :math:`Q_l`, which is a
rotationally invariant non-negative amplitude obtained by summing
over all the components of degree *l*\ .
@ -181,13 +181,13 @@ values for each atom will be added to the output array, which are real numbers.
If the keyword *components* is set, then the real and imaginary parts
of each component of *normalized* :math:`\hat{Y}_{lm}` will be added to the
output array in the following order: :math:`{\rm Re}(\hat{Y}_{-m}), {\rm Im}(\hat{Y}_{-m}),
{\rm Re}(\hat{Y}_{-m+1}), {\rm Im}(\hat{Y}_{-m+1}), \dots , {\rm Re}(\hat{Y}_m), {\rm Im}(\hat{Y}_m)`.
output array in the following order: :math:`{\rm Re}(\hat{Y}_{-m}), {\rm Im}(\hat{Y}_{-m}),
{\rm Re}(\hat{Y}_{-m+1}), {\rm Im}(\hat{Y}_{-m+1}), \dots , {\rm Re}(\hat{Y}_m), {\rm Im}(\hat{Y}_m)`.
In summary, the per-atom array will contain *nlvalues* columns, followed by
an additional *nlvalues* columns if *wl* is set to yes, followed by
an additional *nlvalues* columns if *wl/hat* is set to yes, followed
by an additional 2\*(2\* *ldegree*\ +1) columns if the *components*
by an additional 2\*(2\* *ldegree*\ +1) columns if the *components*
keyword is set.
These values can be accessed by any command that uses per-atom values

38
doc/src/pair_mliap.rst
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@ -16,19 +16,19 @@ Examples
.. code-block:: LAMMPS
pair_style mliap model linear InP.mliap.model descriptor sna InP.mliap.descriptor
pair_style mliap model quadratic W.mliap.model descriptor sna W.mliap.descriptor
pair_style mliap model quadratic W.mliap.model descriptor sna W.mliap.descriptor
pair_coeff * * In P
Description
"""""""""""
Pair style *mliap* provides a general interface to families of
machine-learning interatomic potentials. It provides separate
Pair style *mliap* provides a general interface to families of
machine-learning interatomic potentials. It provides separate
definitions of the interatomic potential functional form (*model*)
and the geometric quantities that characterize the atomic positions
(*descriptor*). By defining *model* and *descriptor* separately,
(*descriptor*). By defining *model* and *descriptor* separately,
it is possible to use many different models with a given descriptor,
or many different descriptors with a given model. Currently, the pair_style
or many different descriptors with a given model. Currently, the pair_style
supports just two models, *linear* and *quadratic*,
and one descriptor, *sna*, the SNAP descriptor used by :doc:`pair_style snap <pair_snap>`, including the linear, quadratic,
and chem variants. Work is currently underway to extend
@ -37,23 +37,23 @@ and it is also straightforward to add new descriptor styles.
The pair_style *mliap* command must be followed by two keywords
*model* and *descriptor* in either order. A single
*pair_coeff* command is also required. The first 2 arguments
*pair_coeff* command is also required. The first 2 arguments
must be \* \* so as to span all LAMMPS atom types.
This is followed by a list of N arguments
that specify the mapping of MLIAP
element names to LAMMPS atom types,
element names to LAMMPS atom types,
where N is the number of LAMMPS atom types.
The *model* keyword is followed by a model style, currently limited to
either *linear* or *quadratic*. In both cases,
this is followed by a single argument specifying the model filename containing the
linear or quadratic coefficients for a set of elements.
this is followed by a single argument specifying the model filename containing the
linear or quadratic coefficients for a set of elements.
The model filename usually ends in the *.mliap.model* extension.
It may contain coefficients for many elements. The only requirement is that it
contain at least those element names appearing in the
*pair_coeff* command.
The top of the model file can contain any number of blank and comment lines (start with #),
The top of the model file can contain any number of blank and comment lines (start with #),
but follows a strict format after that. The first non-blank non-comment
line must contain two integers:
@ -64,20 +64,20 @@ This is followed by one block for each of the *nelem* elements.
Each block consists of *ncoeff* coefficients, one per line.
Note that this format is similar, but not identical to that used
for the :doc:`pair_style snap <pair_snap>` coefficient file.
Specifically, the line containing the element weight and radius is omitted,
Specifically, the line containing the element weight and radius is omitted,
since these are handled by the *descriptor*.
The *descriptor* keyword is followed by a descriptor style, and additional arguments.
Currently the only descriptor style is *sna*, indicating the bispectrum component
descriptors used by the Spectral Neighbor Analysis Potential (SNAP) potentials of
Currently the only descriptor style is *sna*, indicating the bispectrum component
descriptors used by the Spectral Neighbor Analysis Potential (SNAP) potentials of
:doc:`pair_style snap <pair_snap>`.
The \'p\' in SNAP is dropped, because keywords that match pair_styles are silently stripped
out by the LAMMPS command parser. A single additional argument specifies the descriptor filename
containing the parameters and setting used by the SNAP descriptor.
The \'p\' in SNAP is dropped, because keywords that match pair_styles are silently stripped
out by the LAMMPS command parser. A single additional argument specifies the descriptor filename
containing the parameters and setting used by the SNAP descriptor.
The descriptor filename usually ends in the *.mliap.descriptor* extension.
The SNAP descriptor file closely follows the format of the
:doc:`pair_style snap <pair_snap>` parameter file.
The SNAP descriptor file closely follows the format of the
:doc:`pair_style snap <pair_snap>` parameter file.
The file can contain blank and comment lines (start
with #) anywhere. Each non-blank non-comment line must contain one
keyword/value pair. The required keywords are *rcutfac* and
@ -87,7 +87,7 @@ In addition, the SNAP descriptor file must contain
the *nelems*, *elems*, *radelems*, and *welems* keywords.
The *nelems* keyword specifies the number of elements
provided in the other three keywords.
The *elems* keyword is followed by a list of *nelems*
The *elems* keyword is followed by a list of *nelems*
element names that must include the element
names appearing in the *pair_coeff* command,
but can contain other names too.

28
doc/src/pair_snap.rst
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@ -25,9 +25,9 @@ Description
"""""""""""
Pair style *snap* defines the spectral
neighbor analysis potential (SNAP), a machine-learning
neighbor analysis potential (SNAP), a machine-learning
interatomic potential :ref:`(Thompson) <Thompson20142>`.
Like the GAP framework of Bartok et al. :ref:`(Bartok2010) <Bartok20102>`,
Like the GAP framework of Bartok et al. :ref:`(Bartok2010) <Bartok20102>`,
SNAP uses bispectrum components
to characterize the local neighborhood of each atom
in a very general way. The mathematical definition of the
@ -139,7 +139,7 @@ The SNAP parameter file can contain blank and comment lines (start
with #) anywhere. Each non-blank non-comment line must contain one
keyword/value pair. The required keywords are *rcutfac* and
*twojmax*\ . Optional keywords are *rfac0*\ , *rmin0*\ ,
*switchflag*\ , *bzeroflag*\ , *quadraticflag*\ , *chemflag*\ ,
*switchflag*\ , *bzeroflag*\ , *quadraticflag*\ , *chemflag*\ ,
*bnormflag*\ , *wselfallflag*\ , and *chunksize*\ .
The default values for these keywords are
@ -154,34 +154,34 @@ The default values for these keywords are
* *wselfallflag* = 0
* *chunksize* = 2000
If *quadraticflag* is set to 1, then the SNAP energy expression includes additional quadratic terms
If *quadraticflag* is set to 1, then the SNAP energy expression includes additional quadratic terms
that have been shown to increase the overall accuracy of the potential without much increase
in computational cost :ref:`(Wood) <Wood20182>`.
in computational cost :ref:`(Wood) <Wood20182>`.
.. math::
E^i_{SNAP}(\mathbf{B}^i) = \beta^{\mu_i}_0 + \boldsymbol{\beta}^{\mu_i} \cdot \mathbf{B}_i + \frac{1}{2}\mathbf{B}^t_i \cdot \boldsymbol{\alpha}^{\mu_i} \cdot \mathbf{B}_i
where :math:`\mathbf{B}_i` is the *K*-vector of bispectrum components,
:math:`\boldsymbol{\beta}^{\mu_i}` is the *K*-vector of linear coefficients
for element :math:`\mu_i`, and :math:`\boldsymbol{\alpha}^{\mu_i}`
where :math:`\mathbf{B}_i` is the *K*-vector of bispectrum components,
:math:`\boldsymbol{\beta}^{\mu_i}` is the *K*-vector of linear coefficients
for element :math:`\mu_i`, and :math:`\boldsymbol{\alpha}^{\mu_i}`
is the symmetric *K* by *K* matrix of quadratic coefficients.
The SNAP element file should contain *K*\ (\ *K*\ +1)/2 additional coefficients
for each element, the upper-triangular elements of :math:`\boldsymbol{\alpha}^{\mu_i}`.
If *chemflag* is set to 1, then the energy expression is written in terms of explicit multi-element bispectrum
components indexed on ordered triplets of elements, which has been shown to increase the ability of the SNAP
potential to capture energy differences in chemically complex systems,
potential to capture energy differences in chemically complex systems,
at the expense of a significant increase in computational cost :ref:`(Cusentino) <Cusentino20202>`.
.. math::
E^i_{SNAP}(\mathbf{B}^i) = \beta^{\mu_i}_0 + \sum_{\kappa,\lambda,\mu} \boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i} \cdot \mathbf{B}^{\kappa\lambda\mu}_i
E^i_{SNAP}(\mathbf{B}^i) = \beta^{\mu_i}_0 + \sum_{\kappa,\lambda,\mu} \boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i} \cdot \mathbf{B}^{\kappa\lambda\mu}_i
where :math:`\mathbf{B}^{\kappa\lambda\mu}_i` is the *K*-vector of bispectrum components
for neighbors of elements :math:`\kappa`, :math:`\lambda`, and :math:`\mu` and
:math:`\boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i}` is the corresponding *K*-vector
of linear coefficients for element :math:`\mu_i`. The SNAP element file should contain
where :math:`\mathbf{B}^{\kappa\lambda\mu}_i` is the *K*-vector of bispectrum components
for neighbors of elements :math:`\kappa`, :math:`\lambda`, and :math:`\mu` and
:math:`\boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i}` is the corresponding *K*-vector
of linear coefficients for element :math:`\mu_i`. The SNAP element file should contain
a total of :math:`K N_{elem}^3` coefficients for each of the :math:`N_{elem}` elements.
The keyword *chunksize* is only applicable when using the

4
src/KOKKOS/pair_snap_kokkos_impl.h
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@ -632,8 +632,8 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeNeigh,const typen
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPBeta,const int& ii) const {
if (ii >= chunk_size) return;
if (ii >= chunk_size) return;
const int iatom_mod = ii % 32;
const int iatom_div = ii / 32;

6
src/KOKKOS/sna_kokkos.h
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@ -160,17 +160,17 @@ inline
t_sna_3c_ll ulist;
t_sna_3c_ll ylist;
// derivatives of data
t_sna_4c3_ll dulist;
// Modified structures for GPU backend
t_sna_3d_ll ulisttot_re; // split real,
t_sna_3d_ll ulisttot_im; // imag
t_sna_4c_ll ulisttot_pack; // AoSoA layout
t_sna_4c_ll zlist_pack; // AoSoA layout
t_sna_4d_ll blist_pack;
t_sna_4d_ll ylist_pack_re; // split real,
t_sna_4d_ll ylist_pack_re; // split real,
t_sna_4d_ll ylist_pack_im; // imag AoSoA layout
int idxcg_max, idxu_max, idxz_max, idxb_max;

16
src/KOKKOS/sna_kokkos_impl.h
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@ -295,7 +295,7 @@ void SNAKokkos<DeviceType>::pre_ui(const typename Kokkos::TeamPolicy<DeviceType>
// if m is on the "diagonal", initialize it with the self energy.
// Otherwise zero it out
double re_part = 0.;
double re_part = 0.;
if (m % (j+2) == 0 && (!chem_flag || ielem == jelem || wselfall_flag)) { re_part = wself; }
ulisttot_re(jjup, jelem, iatom) = re_part;
@ -436,7 +436,7 @@ void SNAKokkos<DeviceType>::compute_ui(const typename Kokkos::TeamPolicy<DeviceT
} else {
u_accum.re = -u_accum.re;
}
buf2[jju_shared_flip] = u_accum;
// split re, im to get fully coalesced atomic add
@ -607,7 +607,7 @@ void SNAKokkos<DeviceType>::compute_bi(const int& iatom_mod, const int& jjb, con
blist_pack(iatom_mod, jjb, itriple, iatom_div) = sumzu;
//} // end loop over j
//} // end loop over j1, j2
itriple++;
itriple++;
} // end loop over elem3
idouble++;
} // end loop over elem2
@ -788,7 +788,7 @@ void SNAKokkos<DeviceType>::compute_fused_deidrj(const typename Kokkos::TeamPoli
// single has a warp barrier at the end
Kokkos::single(Kokkos::PerThread(team), [=]() {
ulist_buf1[0] = {1., 0.};
dulist_buf1[0] = {0., 0.};
});
@ -878,7 +878,7 @@ void SNAKokkos<DeviceType>::compute_fused_deidrj(const typename Kokkos::TeamPoli
// u[ma-j][mb-j] = (-1)^(ma-mb)*Conj([u[ma][mb])
if (j%2==1 && mb+1==n_mb) {
int sign_factor = (((ma+mb)%2==0)?1:-1);
const int jju_shared_flip = (j+1-mb)*(j+1)-(ma+1);
if (sign_factor == 1) {
@ -1138,7 +1138,7 @@ void SNAKokkos<DeviceType>::compute_bi_cpu(const typename Kokkos::TeamPolicy<Dev
if (elem1 == elem2 && elem1 == elem3) {
sumzu -= bzero[j];
}
} else {
} else {
sumzu -= bzero[j];
}
}
@ -1153,7 +1153,7 @@ void SNAKokkos<DeviceType>::compute_bi_cpu(const typename Kokkos::TeamPolicy<Dev
idouble++;
} // end loop over elem2
} // end loop over elem1
}
/* ----------------------------------------------------------------------
@ -2036,7 +2036,7 @@ double SNAKokkos<DeviceType>::memory_usage()
#ifdef KOKKOS_ENABLE_CUDA
if (std::is_same<DeviceType,Kokkos::Cuda>::value) {
bytes += natom * idxu_max * nelements * sizeof(double); // ulisttot_re
bytes += natom * idxu_max * nelements * sizeof(double); // ulisttot_im
bytes += natom_pad * idxu_max * nelements * sizeof(double) * 2; // ulisttot_pack

2
src/KSPACE/fix_tune_kspace.cpp
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@ -149,7 +149,7 @@ void FixTuneKspace::pre_exchange()
update_pair_style(new_pair_style,pair_cut_coul);
update_kspace_style(new_kspace_style,new_acc_str);
} else if (niter == 4) {
store_old_kspace_settings();
store_old_kspace_settings();
if (comm->me == 0)
utils::logmesg(lmp,fmt::format("ewald_time = {}\n"
"pppm_time = {}\n"

18
src/MLIAP/mliap_descriptor_snap.cpp
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@ -36,7 +36,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
MLIAPDescriptorSNAP::MLIAPDescriptorSNAP(LAMMPS *lmp, char *paramfilename):
MLIAPDescriptorSNAP::MLIAPDescriptorSNAP(LAMMPS *lmp, char *paramfilename):
MLIAPDescriptor(lmp)
{
nelements = 0;
@ -242,13 +242,13 @@ void MLIAPDescriptorSNAP::backward(PairMLIAP* pairmliap, NeighList* list, double
// add in gloabl and per-atom virial contributions
// this is optional and has no effect on force calculation
if (vflag)
pairmliap->v_tally(i,j,
fij[0],fij[1],fij[2],
-snaptr->rij[jj][0],-snaptr->rij[jj][1],
-snaptr->rij[jj][2]);
}
}
@ -338,8 +338,8 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename)
utils::logmesg(lmp, fmt::format("SNAP keyword {} {} \n", keywd, keyval));
}
// check for keywords with one value per element
// check for keywords with one value per element
if (strcmp(keywd,"elems") == 0 ||
strcmp(keywd,"radelems") == 0 ||
strcmp(keywd,"welems") == 0) {
@ -372,9 +372,9 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename)
} else {
// all other keywords take one value
// all other keywords take one value
if (nwords != 2)
if (nwords != 2)
error->all(FLERR,"Incorrect SNAP parameter file");
if (strcmp(keywd,"nelems") == 0) {
@ -408,8 +408,8 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename)
}
}
if (!rcutfacflag || !twojmaxflag || !nelementsflag ||
if (!rcutfacflag || !twojmaxflag || !nelementsflag ||
!elementsflag || !radelemflag || !wjelemflag)
error->all(FLERR,"Incorrect SNAP parameter file");

4
src/MLIAP/mliap_model_linear.cpp
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@ -28,7 +28,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
MLIAPModelLinear::MLIAPModelLinear(LAMMPS* lmp, char* coefffilename) :
MLIAPModelLinear::MLIAPModelLinear(LAMMPS* lmp, char* coefffilename) :
MLIAPModel(lmp, coefffilename)
{
nonlinearflag = 0;
@ -71,7 +71,7 @@ void MLIAPModelLinear::gradient(PairMLIAP* pairmliap, NeighList* list, double **
for (int icoeff = 0; icoeff < ndescriptors; icoeff++)
etmp += coeffi[icoeff+1]*descriptors[ii][icoeff];
pairmliap->e_tally(i,etmp);
}
}

4
src/MLIAP/mliap_model_quadratic.cpp
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@ -28,7 +28,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
MLIAPModelQuadratic::MLIAPModelQuadratic(LAMMPS* lmp, char* coefffilename) :
MLIAPModelQuadratic::MLIAPModelQuadratic(LAMMPS* lmp, char* coefffilename) :
MLIAPModel(lmp, coefffilename)
{
nonlinearflag = 1;
@ -72,7 +72,7 @@ void MLIAPModelQuadratic::gradient(PairMLIAP* pairmliap, NeighList* list, double
// add in contributions to global and per-atom energy
// this is optional and has no effect on force calculation
if (eflag) {
// energy of atom I

4
src/MLIAP/pair_mliap.cpp
View File

@ -93,10 +93,10 @@ void PairMLIAP::compute(int eflag, int vflag)
model->gradient(this, list, descriptors, beta, eflag);
// calculate force contributions beta_i*dB_i/dR_j
descriptor->backward(this, list, beta, vflag);
// calculate stress
// calculate stress
if (vflag_fdotr) virial_fdotr_compute();
}

2
src/MLIAP/pair_mliap.h
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@ -45,7 +45,7 @@ protected:
double** beta; // betas for all atoms in list
double** descriptors; // descriptors for all atoms in list
int ndescriptors; // number of descriptors
int ndescriptors; // number of descriptors
int beta_max; // number of atoms allocated for beta, descriptors
class MLIAPModel* model;

2
src/REPLICA/fix_hyper_local.cpp
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@ -1683,7 +1683,7 @@ double FixHyperLocal::compute_vector(int i)
return (double) allovercount;
}
*/
return 0.0;
}

2
src/USER-MISC/pair_tersoff_table.cpp
View File

@ -852,7 +852,7 @@ void PairTersoffTable::read_file(char *file)
if (comm->me == 0) {
PotentialFileReader reader(lmp, file, "TersoffTable", unit_convert_flag);
char *line;
// transparently convert units for supported conversions
int unit_convert = reader.get_unit_convert();