lijiext
/
lammps
mirror of https://github.com/lammps/lammps.git
1
0
Fork 1
Code Issues Packages Projects Releases Wiki Activity

Merge pull request #2203 from akohlmey/collected-small-changes 

Various small fixes and cleanups. Bugfixes for atom style hybrid
This commit is contained in:
Axel Kohlmeyer 2020-07-01 06:24:28 -04:00 committed by GitHub
parent a73f1d4f03 0a9dd81288
commit 558d2eb84f
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
37 changed files with 158 additions and 165 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
doc/src/compute_orientorder_atom.rst
View File

@ -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
View File

@ -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
View File

@ -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

32
src/BODY/pair_body_rounded_polygon.cpp
View File

@ -236,7 +236,7 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
edge[jefirst+nj][4] = 0;
}
int interact, num_contacts, done;
int num_contacts, done;
double delta_a, j_a;
Contact contact_list[MAX_CONTACTS];
@ -244,15 +244,13 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
// check interaction between i's vertices and j' edges
interact = vertex_against_edge(i, j, k_nij, k_naij,
x, f, torque, tag, contact_list,
num_contacts, evdwl, facc);
vertex_against_edge(i, j, k_nij, k_naij, x, f, torque, tag,
contact_list, num_contacts, evdwl, facc);
// check interaction between j's vertices and i' edges
interact = vertex_against_edge(j, i, k_nij, k_naij,
x, f, torque, tag, contact_list,
num_contacts, evdwl, facc);
vertex_against_edge(j, i, k_nij, k_naij, x, f, torque, tag,
contact_list, num_contacts, evdwl, facc);
if (num_contacts >= 2) {
@ -595,7 +593,7 @@ void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j,
{
double rradi,rradj;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double rij,rsqinv,R,fx,fy,fz,fpair,shift,energy;
double rij,rsqinv,R,fx,fy,fz,fn[3],ft[3],fpair,shift,energy;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
@ -641,6 +639,23 @@ void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j,
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// normal friction term at contact
fn[0] = -c_n * vn1;
fn[1] = -c_n * vn2;
fn[2] = -c_n * vn3;
// tangential friction term at contact,
// excluding the tangential deformation term for now
ft[0] = -c_t * vt1;
ft[1] = -c_t * vt2;
ft[2] = -c_t * vt3;
fx += fn[0] + ft[0];
fy += fn[1] + ft[1];
fz += fn[2] + ft[2];
}
f[i][0] += fx;
@ -1349,4 +1364,3 @@ void PairBodyRoundedPolygon::distance(const double* x2, const double* x1,
+ (x2[1] - x1[1]) * (x2[1] - x1[1])
+ (x2[2] - x1[2]) * (x2[2] - x1[2]));
}

12
src/KOKKOS/atom_vec_kokkos.h
View File

@ -103,14 +103,14 @@ class AtomVecKokkos : public AtomVec {
ExecutionSpace space) = 0;
virtual int
pack_border_vel_kokkos(int n, DAT::tdual_int_2d k_sendlist,
DAT::tdual_xfloat_2d buf,int iswap,
int pbc_flag, int *pbc, ExecutionSpace space) { return 0; }
pack_border_vel_kokkos(int /*n*/, DAT::tdual_int_2d /*k_sendlist*/,
DAT::tdual_xfloat_2d /*buf*/,int /*iswap*/,
int /*pbc_flag*/, int * /*pbc*/, ExecutionSpace /*space*/) { return 0; }
virtual void
unpack_border_vel_kokkos(const int &n, const int &nfirst,
const DAT::tdual_xfloat_2d &buf,
ExecutionSpace space) {}
unpack_border_vel_kokkos(const int &/*n*/, const int & /*nfirst*/,
const DAT::tdual_xfloat_2d & /*buf*/,
ExecutionSpace /*space*/) {}
virtual int
pack_exchange_kokkos(const int &nsend, DAT::tdual_xfloat_2d &buf,

4
src/KOKKOS/kokkos_type.h
View File

@ -272,7 +272,7 @@ template<typename T1, typename T2>
class ScatterViewHelper<Kokkos::Experimental::ScatterDuplicated,T1,T2> {
public:
KOKKOS_INLINE_FUNCTION
static T1 get(const T1 &dup, const T2 &nondup) {
static T1 get(const T1 &dup, const T2 & /*nondup*/) {
return dup;
}
};
@ -1025,7 +1025,7 @@ struct params_lj_coul {
KOKKOS_INLINE_FUNCTION
params_lj_coul(){cut_ljsq=0;cut_coulsq=0;lj1=0;lj2=0;lj3=0;lj4=0;offset=0;};
KOKKOS_INLINE_FUNCTION
params_lj_coul(int i){cut_ljsq=0;cut_coulsq=0;lj1=0;lj2=0;lj3=0;lj4=0;offset=0;};
params_lj_coul(int /*i*/){cut_ljsq=0;cut_coulsq=0;lj1=0;lj2=0;lj3=0;lj4=0;offset=0;};
F_FLOAT cut_ljsq,cut_coulsq,lj1,lj2,lj3,lj4,offset;
};

4
src/KOKKOS/pair_snap_kokkos_impl.h
View File

@ -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
View File

@ -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;

22
src/KOKKOS/sna_kokkos_impl.h
View File

@ -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;
@ -368,7 +368,6 @@ void SNAKokkos<DeviceType>::compute_ui(const typename Kokkos::TeamPolicy<DeviceT
for (int j = 1; j <= twojmax; j++) {
const int jju = idxu_block[j];
const int jjup = idxu_block[j-1];
// fill in left side of matrix layer from previous layer
@ -436,7 +435,7 @@ 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 +606,7 @@ 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 +787,7 @@ 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 +877,7 @@ 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) {
@ -1080,7 +1079,6 @@ void SNAKokkos<DeviceType>::compute_bi_cpu(const typename Kokkos::TeamPolicy<Dev
Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxb_max),
[&] (const int& jjb) {
//for(int jjb = 0; jjb < idxb_max; jjb++) {
const auto jjballoy = itriple;
const int j1 = idxb(jjb, 0);
const int j2 = idxb(jjb, 1);
const int j = idxb(jjb, 2);
@ -1138,7 +1136,7 @@ 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 +1151,7 @@ void SNAKokkos<DeviceType>::compute_bi_cpu(const typename Kokkos::TeamPolicy<Dev
idouble++;
} // end loop over elem2
} // end loop over elem1
}
/* ----------------------------------------------------------------------
@ -2024,7 +2022,6 @@ double SNAKokkos<DeviceType>::memory_usage()
{
int jdimpq = twojmax + 2;
int jdim = twojmax + 1;
int natom_pad = ((natom + 32 - 1) / 32) * 32; // for AoSoA layouts
double bytes;
bytes = 0;
@ -2032,11 +2029,10 @@ double SNAKokkos<DeviceType>::memory_usage()
bytes += jdimpq*jdimpq * sizeof(double); // pqarray
bytes += idxcg_max * sizeof(double); // cglist
#ifdef KOKKOS_ENABLE_CUDA
if (std::is_same<DeviceType,Kokkos::Cuda>::value) {
int natom_pad = ((natom + 32 - 1) / 32) * 32; // for AoSoA layouts
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
View File

@ -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"

1
src/KSPACE/pppm_disp.cpp
View File

@ -316,7 +316,6 @@ void PPPMDisp::init()
for (int i=0; i<=EWALD_MAXORDER; ++i) // transcribe order
if (ewald_order&(1<<i)) { // from pair_style
int k=0;
char str[128];
switch (i) {
case 1:
k = 0; break;

22
src/MLIAP/mliap_descriptor_snap.cpp
View File

@ -36,7 +36,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
MLIAPDescriptorSNAP::MLIAPDescriptorSNAP(LAMMPS *lmp, char *paramfilename):
MLIAPDescriptorSNAP::MLIAPDescriptorSNAP(LAMMPS *lmp, char *paramfilename):
MLIAPDescriptor(lmp)
{
nelements = 0;
@ -149,15 +149,13 @@ void MLIAPDescriptorSNAP::forward(int* map, NeighList* list, double **descriptor
void MLIAPDescriptorSNAP::backward(PairMLIAP* pairmliap, NeighList* list, double **beta, int vflag)
{
int i,j,jnum,ninside;
double delx,dely,delz,evdwl,rsq;
double delx,dely,delz,rsq;
double fij[3];
int *jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
@ -244,13 +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]);
}
}
@ -340,8 +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) {
@ -374,9 +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) {
@ -410,8 +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");

3
src/MLIAP/mliap_model.cpp
View File

@ -142,7 +142,6 @@ void MLIAPModel::read_coeffs(char *coefffilename)
}
if (comm->me == 0) fclose(fpcoeff);
}
/* ----------------------------------------------------------------------
@ -153,9 +152,7 @@ double MLIAPModel::memory_usage()
{
double bytes = 0;
int n = atom->ntypes+1;
bytes += nelements*nparams*sizeof(double); // coeffelem
return bytes;
}

4
src/MLIAP/mliap_model_linear.cpp
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -1683,7 +1683,7 @@ double FixHyperLocal::compute_vector(int i)
return (double) allovercount;
}
*/
return 0.0;
}

4
src/RIGID/fix_rigid_small.cpp
View File

@ -410,9 +410,9 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
if (comm->me == 0) {
if (screen)
fprintf(screen," create bodies CPU = %g secs\n",time2-time1);
fprintf(screen," create bodies CPU = %g seconds\n",time2-time1);
if (logfile)
fprintf(logfile," create bodies CPU = %g secs\n",time2-time1);
fprintf(logfile," create bodies CPU = %g seconds\n",time2-time1);
}
// set nlocal_body and allocate bodies I own

4
src/RIGID/fix_shake.cpp
View File

@ -229,9 +229,9 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
if (comm->me == 0) {
if (screen)
fprintf(screen," find clusters CPU = %g secs\n",time2-time1);
fprintf(screen," find clusters CPU = %g seconds\n",time2-time1);
if (logfile)
fprintf(logfile," find clusters CPU = %g secs\n",time2-time1);
fprintf(logfile," find clusters CPU = %g seconds\n",time2-time1);
}
// initialize list of SHAKE clusters to constrain

2
src/SNAP/compute_sna_atom.cpp
View File

@ -259,7 +259,7 @@ void ComputeSNAAtom::compute_peratom()
int jtype = type[j];
int jelem = 0;
if (chemflag)
int jelem = map[jtype];
jelem = map[jtype];
if (rsq < cutsq[itype][jtype] && rsq>1e-20) {
snaptr->rij[ninside][0] = delx;
snaptr->rij[ninside][1] = dely;

22
src/USER-CGDNA/bond_oxdna_fene.cpp
View File

@ -328,29 +328,9 @@ void BondOxdnaFene::coeff(int narg, char **arg)
void BondOxdnaFene::init_style()
{
/* special bonds have to be lj = 0 1 1 and coul = 1 1 1 to exclude
the ss excluded volume interaction between nearest neighbors */
force->special_lj[1] = 0.0;
force->special_lj[2] = 1.0;
force->special_lj[3] = 1.0;
force->special_coul[1] = 1.0;
force->special_coul[2] = 1.0;
force->special_coul[3] = 1.0;
fprintf(screen,"Finding 1-2 1-3 1-4 neighbors ...\n"
" Special bond factors lj: %-10g %-10g %-10g\n"
" Special bond factors coul: %-10g %-10g %-10g\n",
force->special_lj[1],force->special_lj[2],force->special_lj[3],
force->special_coul[1],force->special_coul[2],force->special_coul[3]);
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0 ||
force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 || force->special_coul[3] != 1.0)
{
if (comm->me == 0)
error->warning(FLERR,"Use special bonds lj = 0,1,1 and coul = 1,1,1 with bond style oxdna/fene");
}
error->all(FLERR,"Must use 'special_bonds lj 0 1 1 coul 1 1 1' with bond style oxdna/fene");
}
/* ---------------------------------------------------------------------- */

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();

10
src/atom_vec_hybrid.cpp
View File

@ -57,8 +57,6 @@ AtomVecHybrid::~AtomVecHybrid()
delete [] styles;
for (int k = 0; k < nstyles; k++) delete [] keywords[k];
delete [] keywords;
for (int k = 0; k < nstyles_bonus; k++) delete styles_bonus[k];
delete [] styles_bonus;
if (!fields_allocated) return;
@ -225,6 +223,7 @@ void AtomVecHybrid::process_args(int narg, char **arg)
// set bonus_flag if any substyle has bonus data
// set nstyles_bonus & styles_bonus
// sum two sizes over contributions from each substyle with bonus data.
nstyles_bonus = 0;
for (int k = 0; k < nstyles; k++)
@ -234,9 +233,14 @@ void AtomVecHybrid::process_args(int narg, char **arg)
bonus_flag = 1;
styles_bonus = new AtomVec*[nstyles_bonus];
nstyles_bonus = 0;
size_forward_bonus = 0;
size_border_bonus = 0;
for (int k = 0; k < nstyles; k++) {
if (styles[k]->bonus_flag)
if (styles[k]->bonus_flag) {
styles_bonus[nstyles_bonus++] = styles[k];
size_forward_bonus += styles[k]->size_forward_bonus;
size_border_bonus += styles[k]->size_border_bonus;
}
}
}

11
src/domain.cpp
View File

@ -1939,12 +1939,13 @@ void Domain::print_box(const std::string &prefix)
if (comm->me == 0) {
std::string mesg = prefix;
if (triclinic == 0) {
mesg += fmt::format("orthogonal box = ({} {} {}) to ({} {} {})\n",
boxlo[0],boxlo[1],boxlo[2],
boxhi[0],boxhi[1],boxhi[2]);
mesg += fmt::format("orthogonal box = ({:.8g} {:.8g} {:.8g}) to "
"({:.8g} {:.8g} {:.8g})\n",boxlo[0],boxlo[1],
boxlo[2],boxhi[0],boxhi[1],boxhi[2]);
} else {
mesg += fmt::format("triclinic box = ({} {} {}) to ({} {} {}) "
"with tilt ({} {} {})\n",boxlo[0],boxlo[1],
mesg += fmt::format("triclinic box = ({:.8g} {:.8g} {:.8g}) to "
"({:.8g} {:.8g} {:.8g}) with tilt "
"({:.8g} {:.8g} {:.8g})\n",boxlo[0],boxlo[1],
boxlo[2],boxhi[0],boxhi[1],boxhi[2],xy,xz,yz);
}
utils::logmesg(lmp,mesg);

32
src/fix_adapt.cpp
View File

@ -140,12 +140,12 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 2;
} else if (strcmp(arg[iarg],"atom") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
adapt[nadapt].which = ATOM;
if (strcmp(arg[iarg+1],"diameter") == 0 ||
strcmp(arg[iarg+1],"diameter/disc") == 0) {
strcmp(arg[iarg+1],"diameter/disc") == 0) {
adapt[nadapt].aparam = DIAMETER;
diamflag = 1;
discflag = 0;
@ -195,10 +195,10 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
// if scaleflag set with diameter or charge adaptation,
// then previous step scale factors are written to restart file
// initialize them here in case one is used and other is never defined
if (scaleflag && (diamflag || chgflag)) restart_global = 1;
previous_diam_scale = previous_chg_scale = 1.0;
// allocate pair style arrays
int n = atom->ntypes;
@ -452,7 +452,7 @@ void FixAdapt::init()
}
}
}
if (restart_reset) restart_reset = 0;
// make copy of original pair/bond array values
@ -586,9 +586,9 @@ void FixAdapt::change_settings()
// reset radius to new value, for both owned and ghost atoms
// also reset rmass to new value assuming density remains constant
// for scaleflag, previous_diam_scale is the scale factor on previous step
if (ad->aparam == DIAMETER) {
double density,scale;
double scale;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
@ -608,7 +608,7 @@ void FixAdapt::change_settings()
else radius[i] = 0.5*value;
}
}
if (scaleflag) previous_diam_scale = value;
// reset charge to new value, for both owned and ghost atoms
@ -621,15 +621,15 @@ void FixAdapt::change_settings()
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (scaleflag) scale = value / previous_chg_scale;
if (scaleflag) scale = value / previous_chg_scale;
for (i = 0; i < nall; i++) {
if (mask[i] & groupbit) {
if (scaleflag) q[i] *= scale;
else q[i] = value;
}
}
}
if (scaleflag) previous_chg_scale = value;
}
}
@ -691,14 +691,14 @@ void FixAdapt::restore_settings()
} else if (ad->which == ATOM) {
if (diamflag) {
double density,scale;
double scale;
double *vec = fix_diam->vstore;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (scaleflag) scale = previous_diam_scale;
for (int i = 0; i < nlocal; i++)
@ -745,7 +745,7 @@ void FixAdapt::set_arrays(int i)
void FixAdapt::write_restart(FILE *fp)
{
int size = 2*sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(&previous_diam_scale,sizeof(double),1,fp);
fwrite(&previous_chg_scale,sizeof(double),1,fp);
@ -758,7 +758,7 @@ void FixAdapt::write_restart(FILE *fp)
void FixAdapt::restart(char *buf)
{
double *dbuf = (double *) buf;
previous_diam_scale = dbuf[0];
previous_chg_scale = dbuf[1];
}

1
src/info.cpp
View File

@ -793,7 +793,6 @@ bool Info::is_active(const char *category, const char *name)
{
if ((category == NULL) || (name == NULL)) return false;
const char *style = "none";
const int len = strlen(name);
if (strcmp(category,"package") == 0) {
if (strcmp(name,"gpu") == 0) {

3
src/lattice.cpp
View File

@ -304,7 +304,8 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
// print lattice spacings
if (comm->me == 0)
utils::logmesg(lmp,fmt::format("Lattice spacing in x,y,z = {} {} {}\n",
utils::logmesg(lmp,fmt::format("Lattice spacing in x,y,z = "
"{:.8g} {:.8g} {:.8g}\n",
xlattice,ylattice,zlattice));
}

8
src/neighbor.cpp
View File

@ -1438,7 +1438,7 @@ void Neighbor::init_topology()
void Neighbor::print_pairwise_info()
{
int i,m;
int i;
NeighRequest *rq;
const double cutghost = MAX(cutneighmax,comm->cutghostuser);
@ -1466,10 +1466,10 @@ void Neighbor::print_pairwise_info()
every,delay,dist_check ? "yes" : "no");
out += fmt::format(" max neighbors/atom: {}, page size: {}\n",
oneatom, pgsize);
out += fmt::format(" master list distance cutoff = {}\n",cutneighmax);
out += fmt::format(" ghost atom cutoff = {}\n",cutghost);
out += fmt::format(" master list distance cutoff = {:.8g}\n",cutneighmax);
out += fmt::format(" ghost atom cutoff = {:.8g}\n",cutghost);
if (style != Neighbor::NSQ)
out += fmt::format(" binsize = {}, bins = {} {} {}\n",binsize,
out += fmt::format(" binsize = {:.8g}, bins = {:g} {:g} {:g}\n",binsize,
ceil(bbox[0]/binsize), ceil(bbox[1]/binsize),
ceil(bbox[2]/binsize));

1
src/pair_table.cpp
View File

@ -70,7 +70,6 @@ void PairTable::compute(int eflag, int vflag)
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,factor_lj,fraction,value,a,b;
char estr[128];
int *ilist,*jlist,*numneigh,**firstneigh;
Table *tb;

2
src/read_data.cpp
View File

@ -897,7 +897,7 @@ void ReadData::command(int narg, char **arg)
MPI_Barrier(world);
if (comm->me == 0)
utils::logmesg(lmp,fmt::format(" read_data CPU = {:.3f} secs\n",
utils::logmesg(lmp,fmt::format(" read_data CPU = {:.3f} seconds\n",
MPI_Wtime()-time1));
}

2
src/read_restart.cpp
View File

@ -511,7 +511,7 @@ void ReadRestart::command(int narg, char **arg)
MPI_Barrier(world);
if (comm->me == 0)
utils::logmesg(lmp,fmt::format(" read_restart CPU = {:.3f} secs\n",
utils::logmesg(lmp,fmt::format(" read_restart CPU = {:.3f} seconds\n",
MPI_Wtime()-time1));
}

2
src/replicate.cpp
View File

@ -779,6 +779,6 @@ void Replicate::command(int narg, char **arg)
MPI_Barrier(world);
if (me == 0)
utils::logmesg(lmp,fmt::format(" replicate CPU = {:.3f} secs\n",
utils::logmesg(lmp,fmt::format(" replicate CPU = {:.3f} seconds\n",
MPI_Wtime()-time1));
}

6
src/special.cpp
View File

@ -63,8 +63,8 @@ void Special::build()
const double * const special_lj = force->special_lj;
const double * const special_coul = force->special_coul;
fmt::print(screen,"Finding 1-2 1-3 1-4 neighbors ...\n"
" special bond factors lj: {:<10g} {:<10g} {:<10g}\n"
" special bond factors coul: {:<10g} {:<10g} {:<10g}\n",
" special bond factors lj: {:<8g} {:<8g} {:<8g}\n"
" special bond factors coul: {:<8g} {:<8g} {:<8g}\n",
special_lj[1],special_lj[2],special_lj[3],
special_coul[1],special_coul[2],special_coul[3]);
}
@ -1314,6 +1314,6 @@ void Special::fix_alteration()
void Special::timer_output(double time1)
{
if (comm->me == 0)
utils::logmesg(lmp,fmt::format(" special bonds CPU = {:.3f} secs\n",
utils::logmesg(lmp,fmt::format(" special bonds CPU = {:.3f} seconds\n",
MPI_Wtime()-time1));
}

4
src/utils.cpp
View File

@ -549,9 +549,9 @@ bool utils::is_double(const std::string & str) {
std::string utils::path_basename(const std::string & path) {
#if defined(_WIN32)
size_t start = path.find_last_of('/\\');
size_t start = path.find_last_of("/\\");
#else
size_t start = path.find_last_of('/');
size_t start = path.find_last_of("/");
#endif
if (start == std::string::npos) {

5
unittest/force-styles/pair_style.cpp
View File

@ -1007,6 +1007,9 @@ TEST(PairStyle, single)
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
// need to add this dependency
test_config.prerequisites.push_back(std::make_pair("atom", "full"));
// create a LAMMPS instance with standard settings to detect the number of atom types
if (!verbose) ::testing::internal::CaptureStdout();
LAMMPS *lmp = init_lammps(argc, argv, test_config);
@ -1018,8 +1021,10 @@ TEST(PairStyle, single)
for (auto prerequisite : test_config.prerequisites) {
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
}
test_config.prerequisites.pop_back();
GTEST_SKIP();
}
test_config.prerequisites.pop_back();
// gather some information and skip if unsupported
int ntypes = lmp->atom->ntypes;

2
unittest/force-styles/tests/atomic-pair-eam.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 15 Jun 2020
date_generated: Thu Jun 25 12:25:55 202
epsilon: 5e-12
epsilon: 6e-12
prerequisites: ! |
pair eam
pre_commands: ! |