Merge remote-tracking branch 'refs/remotes/origin/chem_snap' into chem_snap
This commit is contained in:
Sievers
@ -30,7 +30,7 @@ Syntax
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* R_1, R_2,... = list of cutoff radii, one for each type (distance units)
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* w_1, w_2,... = list of neighbor weights, one for each type
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* zero or more keyword/value pairs may be appended
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* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag*
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* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag*
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.. parsed-literal::
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@ -44,6 +44,15 @@ Syntax
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*quadraticflag* value = *0* or *1*
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*0* = do not generate quadratic terms
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*1* = generate quadratic terms
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*chem* values = *nelements* *elementlist*
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*nelements* = number of SNAP elements
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*elementlist* = *ntypes* integers in range [0, *nelements*)
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*bnormflag* value = *0* or *1*
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*0* = do not normalize
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*1* = normalize bispectrum components
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*wselfallflag* value = *0* or *1*
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*0* = self-contribution only for element of central atom
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*1* = self-contribution for all elements
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Examples
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""""""""
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@ -54,6 +63,7 @@ Examples
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compute db all sna/atom 1.4 0.95 6 2.0 1.0
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compute vb all sna/atom 1.4 0.95 6 2.0 1.0
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compute snap all snap 1.4 0.95 6 2.0 1.0
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compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 chem 2 0 1
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Description
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"""""""""""
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@ -71,27 +81,26 @@ mathematical definition is given in the paper by Thompson et
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al. :ref:`(Thompson) <Thompson20141>`
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The position of a neighbor atom *i'* relative to a central atom *i* is
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a point within the 3D ball of radius *R_ii' = rcutfac\*(R_i + R_i')*
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a point within the 3D ball of radius :math:`R_{ii'}` = *rcutfac* :math:`(R_i + R_i')`
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Bartok et al. :ref:`(Bartok) <Bartok20101>`, proposed mapping this 3D ball
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onto the 3-sphere, the surface of the unit ball in a four-dimensional
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space. The radial distance *r* within *R_ii'* is mapped on to a third
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polar angle *theta0* defined by,
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polar angle :math:`\theta_0` defined by,
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.. math::
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\theta_0 = {\tt rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
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\theta_0 = {\sf rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
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In this way, all possible neighbor positions are mapped on to a subset
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of the 3-sphere. Points south of the latitude *theta0max=rfac0\*Pi*
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of the 3-sphere. Points south of the latitude :math:`\theta_0` = *rfac0* :math:`\pi`
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are excluded.
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The natural basis for functions on the 3-sphere is formed by the 4D
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hyperspherical harmonics *U\^j_m,m'(theta, phi, theta0).* These
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functions are better known as *D\^j_m,m',* the elements of the Wigner
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The natural basis for functions on the 3-sphere is formed by the
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representatives of *SU(2)*, the matrices :math:`U^j_{m,m'}(\theta, \phi, \theta_0)`.
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These functions are better known as :math:`D^j_{m,m'}`, the elements of the Wigner
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*D*\ -matrices :ref:`(Meremianin <Meremianin2006>`,
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:ref:`Varshalovich) <Varshalovich1987>`.
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:ref:`Varshalovich <Varshalovich1987>`, :ref:`Mason) <Mason2009>`
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The density of neighbors on the 3-sphere can be written as a sum of
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Dirac-delta functions, one for each neighbor, weighted by species and
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radial distance. Expanding this density function as a generalized
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@ -100,20 +109,20 @@ coefficient as
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.. math::
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u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{i'} U^j_{m,m'}(\theta_0,\theta,\phi)}
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u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{\mu_{i'}} U^j_{m,m'}(\theta_0,\theta,\phi)}
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The *w_i'* neighbor weights are dimensionless numbers that are chosen
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to distinguish atoms of different types, while the central atom is
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arbitrarily assigned a unit weight. The function *fc(r)* ensures that
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The :math:`w_{\mu_{i'}}` neighbor weights are dimensionless numbers that depend on
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:math:`\mu_{i'}`, the SNAP element of atom *i'*, while the central atom is
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arbitrarily assigned a unit weight. The function :math:`f_c(r)` ensures that
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the contribution of each neighbor atom goes smoothly to zero at
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*R_ii'*:
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:math:`R_{ii'}`:
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.. math::
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f_c(r) = & \frac{1}{2}(\cos(\pi \frac{r-r_{min0}}{R_{ii'}-r_{min0}}) + 1), r \leq R_{ii'} \\
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= & 0, r > R_{ii'}
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The expansion coefficients *u\^j_m,m'* are complex-valued and they are
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The expansion coefficients :math:`u^j_{m,m'}` are complex-valued and they are
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not directly useful as descriptors, because they are not invariant
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under rotation of the polar coordinate frame. However, the following
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scalar triple products of expansion coefficients can be shown to be
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@ -128,7 +137,8 @@ real-valued and invariant under rotation :ref:`(Bartok) <Bartok20101>`.
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{j_2} {m_2} {m'_2} \end{array}}
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u^{j_1}_{m_1,m'_1} u^{j_2}_{m_2,m'_2}
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The constants *H\^jmm'_j1m1m1'_j2m2m2'* are coupling coefficients,
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The constants :math:`H^{jmm'}_{j_1 m_1 m_{1'},j_2 m_ 2m_{2'}}`
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are coupling coefficients,
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analogous to Clebsch-Gordan coefficients for rotations on the
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2-sphere. These invariants are the components of the bispectrum and
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these are the quantities calculated by the compute *sna/atom*\ . They
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@ -136,13 +146,12 @@ characterize the strength of density correlations at three points on
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the 3-sphere. The j2=0 subset form the power spectrum, which
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characterizes the correlations of two points. The lowest-order
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components describe the coarsest features of the density function,
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while higher-order components reflect finer detail. Note that the
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central atom is included in the expansion, so three point-correlations
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can be either due to three neighbors, or two neighbors and the central
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atom.
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while higher-order components reflect finer detail. Each bispectrum
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component contains terms that depend on the positions of up to 4
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atoms (3 neighbors and the central atom).
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Compute *snad/atom* calculates the derivative of the bispectrum components
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summed separately for each atom type:
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summed separately for each LAMMPS atom type:
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.. math::
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@ -165,7 +174,7 @@ Again, the sum is over all atoms *i'* of atom type *I*\ . For each atom
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virial components, each atom type, and each bispectrum component. See
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section below on output for a detailed explanation.
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Compute *snap* calculates a global array contains information related
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Compute *snap* calculates a global array containing information related
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to all three of the above per-atom computes *sna/atom*\ , *snad/atom*\ ,
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and *snav/atom*\ . The first row of the array contains the summation of
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*sna/atom* over all atoms, but broken out by type. The last six rows
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@ -201,8 +210,8 @@ The argument *rcutfac* is a scale factor that controls the ratio of
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atomic radius to radial cutoff distance.
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The argument *rfac0* and the optional keyword *rmin0* define the
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linear mapping from radial distance to polar angle *theta0* on the
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3-sphere.
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linear mapping from radial distance to polar angle :math:`theta_0` on the
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3-sphere, given above.
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The argument *twojmax* defines which
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bispectrum components are generated. See section below on output for a
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@ -210,7 +219,7 @@ detailed explanation of the number of bispectrum components and the
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ordered in which they are listed.
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The keyword *switchflag* can be used to turn off the switching
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function.
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function :math:`f_c(r)`.
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The keyword *bzeroflag* determines whether or not *B0*\ , the bispectrum
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components of an atom with no neighbors, are subtracted from
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@ -219,13 +228,72 @@ normally only affects compute *sna/atom*\ . However, when
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*quadraticflag* is on, it also affects *snad/atom* and *snav/atom*\ .
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The keyword *quadraticflag* determines whether or not the
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quadratic analogs to the bispectrum quantities are generated.
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quadratic combinations of bispectrum quantities are generated.
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These are formed by taking the outer product of the vector
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of bispectrum components with itself.
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See section below on output for a
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detailed explanation of the number of quadratic terms and the
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ordered in which they are listed.
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The keyword *chem* activates the explicit multi-element variant
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of the SNAP bispectrum components. The argument *nelements*
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specifies the number of SNAP elements that will be handled.
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This is followed by *elementlist*, a list of integers of
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length *ntypes*, with values in the range [0, *nelements* ),
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which maps each LAMMPS type to one of the SNAP elements.
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Note that multiple LAMMPS types can be mapped to the same element,
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and some elements may be mapped by no LAMMPS type. However, in typical
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use cases (training SNAP potentials) the mapping from LAMMPS types
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to elements is one-to-one.
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The explicit multi-element variant invoked by the *chem* keyword
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partitions the density of neighbors into partial densities
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for each chemical element. This is described in detail in the
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paper by :ref:`Cusentino et al. <Cusentino2020>`
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The bispectrum components are indexed on
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ordered triplets of elements:
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.. math::
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B_{j_1,j_2,j}^{\kappa\lambda\mu} =
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\sum_{m_1,m'_1=-j_1}^{j_1}\sum_{m_2,m'_2=-j_2}^{j_2}\sum_{m,m'=-j}^{j} (u^{\mu}_{j,m,m'})^*
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H {\scriptscriptstyle \begin{array}{l} {j} {m} {m'} \\
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{j_1} {m_1} {m'_1} \\
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{j_2} {m_2} {m'_2} \end{array}}
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u^{\kappa}_{j_1,m_1,m'_1} u^{\lambda}_{j_2,m_2,m'_2}
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where :math:`u^{\mu}_{j,m,m'}` is an expansion coefficient for the partial density of neighbors
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of element :math:`\mu`
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.. math::
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u^{\mu}_{j,m,m'} = w^{self}_{\mu_{i}\mu} U^{j,m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{\delta_{\mu\mu_{i'}}f_c(r_{ii'}) w_{\mu_{i'}} U^{j,m,m'}(\theta_0,\theta,\phi)}
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where :math:`w^{self}_{\mu_{i}\mu}` is the self-conribution, which is either 1 or 0
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(see keyword *wselfallflag* below), :math:`\delta_{\mu\mu_{i'}}` indicates
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that the sum is only over neighbor atoms of element :math:`\mu`,
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and all other quantities are the same as those appearing in the
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original equation for :math:`u^j_{m,m'}` given above.
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The keyword *wselfallflag* defines the rule used for the self-contribution.
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If *wselfallflag* is on, then :math:`w^{self}_{\mu_{i}\mu}` = 1. If it is
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off then :math:`w^{self}_{\mu_{i}\mu}` = 0, except in the case
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of :math:`{\mu_{i}=\mu}`, when :math:`w^{self}_{\mu_{i}\mu}` = 1.
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When the *chem* keyword is not used, this keyword has no effect.
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The keyword *bnormflag* determines whether or not the bispectrum
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component :math:`B_{j_1,j_2,j}` is divided by a factor of :math:`2j+1`.
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This normalization simplifies force calculations because of the
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following symmetry relation
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.. math::
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\frac{B_{j_1,j_2,j}}{2j+1} = \frac{B_{j,j_2,j_1}}{2j_1+1} = \frac{B_{j_1,j,j_2}}{2j_2+1}
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|
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This option is typically used in conjunction with the *chem* keyword,
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and LAMMPS will generate a warning if both *chem* and *bnormflag*
|
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are not both set or not both unset.
|
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|
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.. note::
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|
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If you have a bonded system, then the settings of
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@ -257,6 +325,8 @@ described by the following piece of python code:
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for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
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if (j>=j1): print j1/2.,j2/2.,j/2.
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|
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For even twojmax = 2(*m*\ -1), :math:`K = m(m+1)(2m+1)/6`, the *m*\ -th pyramidal number. For odd twojmax = 2 *m*\ -1, :math:`K = m(m+1)(m+2)/3`, twice the *m*\ -th tetrahedral number.
|
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|
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.. note::
|
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|
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the *diagonal* keyword allowing other possible choices
|
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@ -267,16 +337,15 @@ described by the following piece of python code:
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Compute *snad/atom* evaluates a per-atom array. The columns are
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arranged into *ntypes* blocks, listed in order of atom type *I*\ . Each
|
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block contains three sub-blocks corresponding to the *x*\ , *y*\ , and *z*
|
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components of the atom position. Each of these sub-blocks contains
|
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one column for each bispectrum component, the same as for compute
|
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*sna/atom*
|
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components of the atom position. Each of these sub-blocks contains *K*
|
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columns for the *K* bispectrum components, the same as for compute *sna/atom*
|
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|
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Compute *snav/atom* evaluates a per-atom array. The columns are
|
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arranged into *ntypes* blocks, listed in order of atom type *I*\ . Each
|
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block contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ ,
|
||||
*yz*\ , *xz*\ , and *xy* components of the virial tensor in Voigt
|
||||
notation. Each of these sub-blocks contains one column for each
|
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bispectrum component, the same as for compute *sna/atom*
|
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notation. Each of these sub-blocks contains *K*
|
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columns for the *K* bispectrum components, the same as for compute *sna/atom*
|
||||
|
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Compute *snap* evaluates a global array.
|
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The columns are arranged into
|
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@ -312,6 +381,14 @@ of linear terms i.e. linear and quadratic terms are contiguous.
|
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So the nesting order from inside to outside is bispectrum component,
|
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linear then quadratic, vector/tensor component, type.
|
||||
|
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If the *chem* keyword is used, then the data is arranged into :math:`N_{elem}^3`
|
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sub-blocks, each sub-block corresponding to a particular chemical labelling
|
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:math:`\kappa\lambda\mu` with the last label changing fastest.
|
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Each sub-block contains *K* bispectrum components. For the purposes
|
||||
of handling contributions to force, virial, and quadratic combinations,
|
||||
these :math:`N_{elem}^3` sub-blocks are treated as a single block
|
||||
of :math:`K N_{elem}^3` columns.
|
||||
|
||||
These values can be accessed by any command that uses per-atom values
|
||||
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
|
||||
page for an overview of LAMMPS output options.
|
||||
@ -320,7 +397,8 @@ Restrictions
|
||||
""""""""""""
|
||||
|
||||
These computes are part of the SNAP package. They are only enabled if
|
||||
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
|
||||
doc page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
@ -332,6 +410,7 @@ Default
|
||||
|
||||
The optional keyword defaults are *rmin0* = 0,
|
||||
*switchflag* = 1, *bzeroflag* = 1, *quadraticflag* = 0,
|
||||
*bnormflag* = 0, *wselfallflag* = 0
|
||||
|
||||
----------
|
||||
|
||||
@ -352,3 +431,12 @@ available at `arXiv:1409.3880 <http://arxiv.org/abs/1409.3880>`_
|
||||
|
||||
**(Varshalovich)** Varshalovich, Moskalev, Khersonskii, Quantum Theory
|
||||
of Angular Momentum, World Scientific, Singapore (1987).
|
||||
.. _Varshalovich1987:
|
||||
|
||||
.. _Mason2009:
|
||||
|
||||
**(Mason)** J. K. Mason, Acta Cryst A65, 259 (2009).
|
||||
|
||||
.. _Cusentino2020:
|
||||
|
||||
**(Cusentino)** Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)
|
||||
|
||||
@ -24,27 +24,30 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Pair style *snap* computes interactions using the spectral
|
||||
neighbor analysis potential (SNAP) :ref:`(Thompson) <Thompson20142>`.
|
||||
Pair style *snap* defines the spectral
|
||||
neighbor analysis potential (SNAP), a machine-learning
|
||||
interatomic potential :ref:`(Thompson) <Thompson20142>`.
|
||||
Like the GAP framework of Bartok et al. :ref:`(Bartok2010) <Bartok20102>`,
|
||||
:ref:`(Bartok2013) <Bartok2013>` which uses bispectrum components
|
||||
SNAP uses bispectrum components
|
||||
to characterize the local neighborhood of each atom
|
||||
in a very general way. The mathematical definition of the
|
||||
bispectrum calculation used by SNAP is identical
|
||||
to that used by :doc:`compute sna/atom <compute_sna_atom>`.
|
||||
bispectrum calculation and its derivatives w.r.t. atom positions
|
||||
is identical to that used by :doc:`compute snap <compute_sna_atom>`,
|
||||
which is used to fit SNAP potentials to *ab initio* energy, force,
|
||||
and stress data.
|
||||
In SNAP, the total energy is decomposed into a sum over
|
||||
atom energies. The energy of atom *i* is
|
||||
expressed as a weighted sum over bispectrum components.
|
||||
|
||||
.. math::
|
||||
|
||||
E^i_{SNAP}(B_1^i,...,B_K^i) = \beta^{\alpha_i}_0 + \sum_{k=1}^K \beta_k^{\alpha_i} B_k^i
|
||||
E^i_{SNAP}(B_1^i,...,B_K^i) = \beta^{\mu_i}_0 + \sum_{k=1}^K \beta_k^{\mu_i} B_k^i
|
||||
|
||||
where :math:`B_k^i` is the *k*\ -th bispectrum component of atom *i*\ ,
|
||||
and :math:`\beta_k^{\alpha_i}` is the corresponding linear coefficient
|
||||
that depends on :math:\alpha_i`, the SNAP element of atom *i*\ . The
|
||||
and :math:`\beta_k^{\mu_i}` is the corresponding linear coefficient
|
||||
that depends on :math:`\mu_i`, the SNAP element of atom *i*\ . The
|
||||
number of bispectrum components used and their definitions
|
||||
depend on the value of *twojmax*
|
||||
depend on the value of *twojmax* and other parameters
|
||||
defined in the SNAP parameter file described below.
|
||||
The bispectrum calculation is described in more detail
|
||||
in :doc:`compute sna/atom <compute_sna_atom>`.
|
||||
@ -136,17 +139,51 @@ 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*\, and *chunksize*\.
|
||||
*switchflag*\ , *bzeroflag*\ , *quadraticflag*\ , *chemflag*\ ,
|
||||
*bnormflag*\ , *wselfallflag*\ , and *chunksize*\ .
|
||||
|
||||
The default values for these keywords are
|
||||
|
||||
* *rfac0* = 0.99363
|
||||
* *rmin0* = 0.0
|
||||
* *switchflag* = 0
|
||||
* *switchflag* = 1
|
||||
* *bzeroflag* = 1
|
||||
* *quadraticflag* = 1
|
||||
* *quadraticflag* = 0
|
||||
* *chemflag* = 0
|
||||
* *bnormflag* = 0
|
||||
* *wselfallflag* = 0
|
||||
* *chunksize* = 2000
|
||||
|
||||
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>`.
|
||||
|
||||
.. 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}`
|
||||
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,
|
||||
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
|
||||
|
||||
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
|
||||
pair style *snap* with the KOKKOS package and is ignored otherwise.
|
||||
This keyword controls
|
||||
@ -159,10 +196,6 @@ into two passes.
|
||||
Detailed definitions for all the other keywords
|
||||
are given on the :doc:`compute sna/atom <compute_sna_atom>` doc page.
|
||||
|
||||
If *quadraticflag* is set to 1, then the SNAP energy expression includes the quadratic term, 0.5\*B\^t.alpha.B, where alpha is a symmetric *K* by *K* matrix.
|
||||
The SNAP element file should contain *K*\ (\ *K*\ +1)/2 additional coefficients
|
||||
for each element, the upper-triangular elements of alpha.
|
||||
|
||||
.. note::
|
||||
|
||||
The previously used *diagonalstyle* keyword was removed in 2019,
|
||||
@ -221,7 +254,8 @@ Related commands
|
||||
|
||||
:doc:`compute sna/atom <compute_sna_atom>`,
|
||||
:doc:`compute snad/atom <compute_sna_atom>`,
|
||||
:doc:`compute snav/atom <compute_sna_atom>`
|
||||
:doc:`compute snav/atom <compute_sna_atom>`,
|
||||
:doc:`compute snap <compute_sna_atom>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
@ -235,6 +269,10 @@ Related commands
|
||||
|
||||
**(Bartok2010)** Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
|
||||
|
||||
.. _Bartok2013:
|
||||
.. _Wood20182:
|
||||
|
||||
**(Bartok2013)** Bartok, Gillan, Manby, Csanyi, Phys Rev B 87, 184115 (2013).
|
||||
**(Wood)** Wood and Thompson, J Chem Phys, 148, 241721, (2018)
|
||||
|
||||
.. _Cusentino20202:
|
||||
|
||||
**(Cusentino)** Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)
|
||||
|
||||
@ -1,21 +0,0 @@
|
||||
# DATE: 2019-09-18 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019)
|
||||
# Definition of SNAP+ZBL potential.
|
||||
set type 1 charge 1e-08
|
||||
set type 2 charge -1e-08
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.2
|
||||
variable zblz1 equal 49
|
||||
variable zblz2 equal 15
|
||||
variable rcoul equal 10
|
||||
|
||||
# Specify hybrid with SNAP, ZBL, and long-range Coulomb
|
||||
|
||||
pair_style hybrid/overlay coul/long ${rcoul} &
|
||||
zbl ${zblcutinner} ${zblcutouter} &
|
||||
snap
|
||||
pair_coeff * * coul/long
|
||||
pair_coeff 1 1 zbl ${zblz1} ${zblz1}
|
||||
pair_coeff 1 2 zbl ${zblz1} ${zblz2}
|
||||
pair_coeff 2 2 zbl ${zblz2} ${zblz2}
|
||||
pair_coeff * * snap InP_Cusentino_PRB2020.snapcoeff InP_Cusentino_PRB2020.snapparam In P
|
||||
kspace_style ewald 1.0e-5
|
||||
@ -1,13 +0,0 @@
|
||||
|
||||
# required
|
||||
rcutfac 1.0
|
||||
twojmax 6
|
||||
|
||||
# optional
|
||||
rfac0 0.99363
|
||||
rmin0 0.0
|
||||
bzeroflag 1
|
||||
quadraticflag 0
|
||||
wselfallflag 1
|
||||
alloyflag 1
|
||||
|
||||
1
examples/snap/InP_JCPA2020.snap
Symbolic link
1
examples/snap/InP_JCPA2020.snap
Symbolic link
@ -0,0 +1 @@
|
||||
../../potentials/InP_JCPA2020.snap
|
||||
1
examples/snap/InP_JCPA2020.snapcoeff
Symbolic link
1
examples/snap/InP_JCPA2020.snapcoeff
Symbolic link
@ -0,0 +1 @@
|
||||
../../potentials/InP_JCPA2020.snapcoeff
|
||||
1
examples/snap/InP_JCPA2020.snapparam
Symbolic link
1
examples/snap/InP_JCPA2020.snapparam
Symbolic link
@ -0,0 +1 @@
|
||||
../../potentials/InP_JCPA2020.snapparam
|
||||
@ -6,7 +6,6 @@ variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 5.83
|
||||
units metal
|
||||
atom_style charge
|
||||
|
||||
# generate the box and atom positions using a FCC lattice
|
||||
|
||||
@ -26,7 +25,7 @@ mass 2 30.98
|
||||
|
||||
# choose potential
|
||||
|
||||
include InP_Cusentino_PRB2020.snap
|
||||
include InP_JCPA2020.snap
|
||||
|
||||
# Setup output
|
||||
|
||||
156
examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.1
Normal file
156
examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.1
Normal file
@ -0,0 +1,156 @@
|
||||
LAMMPS (2 Jun 2020)
|
||||
# Demonstrate SNAP InP potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 5.83
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a FCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice diamond $a
|
||||
lattice diamond 5.83
|
||||
Lattice spacing in x,y,z = 5.83 5.83 5.83
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
|
||||
Created 512 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 114.76
|
||||
mass 2 30.98
|
||||
|
||||
# choose potential
|
||||
|
||||
include InP_JCPA2020.snap
|
||||
# DATE: 2020-06-01 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020)
|
||||
|
||||
# Definition of SNAP+ZBL potential.
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.2
|
||||
variable zblz1 equal 49
|
||||
variable zblz2 equal 15
|
||||
|
||||
# Specify hybrid with SNAP and ZBL
|
||||
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
|
||||
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
|
||||
pair_style hybrid/overlay zbl 4 4.2 snap
|
||||
pair_coeff 1 1 zbl ${zblz1} ${zblz1}
|
||||
pair_coeff 1 1 zbl 49 ${zblz1}
|
||||
pair_coeff 1 1 zbl 49 49
|
||||
pair_coeff 1 2 zbl ${zblz1} ${zblz2}
|
||||
pair_coeff 1 2 zbl 49 ${zblz2}
|
||||
pair_coeff 1 2 zbl 49 15
|
||||
pair_coeff 2 2 zbl ${zblz2} ${zblz2}
|
||||
pair_coeff 2 2 zbl 15 ${zblz2}
|
||||
pair_coeff 2 2 zbl 15 15
|
||||
pair_coeff * * snap InP_JCPA2020.snapcoeff InP_JCPA2020.snapparam In P
|
||||
Reading potential file InP_JCPA2020.snapcoeff with DATE: 2020-06-01
|
||||
SNAP Element = In, Radius 3.81205, Weight 1
|
||||
SNAP Element = P, Radius 3.82945, Weight 0.929316
|
||||
Reading potential file InP_JCPA2020.snapparam with DATE: 2020-06-01
|
||||
SNAP keyword rcutfac 1.0
|
||||
SNAP keyword twojmax 6
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0.0
|
||||
SNAP keyword bzeroflag 1
|
||||
SNAP keyword quadraticflag 0
|
||||
SNAP keyword wselfallflag 1
|
||||
SNAP keyword chemflag 1
|
||||
SNAP keyword bnormflag 1
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
|
||||
timestep 0.5e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.6589
|
||||
ghost atom cutoff = 8.6589
|
||||
binsize = 4.32945, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair zbl, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair snap, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.027 | 6.027 | 6.027 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -3.4805794 0 -3.4418771 1353.5968
|
||||
10 286.42264 -3.4788274 0 -3.4418767 1586.4881
|
||||
20 250.14148 -3.4741459 0 -3.4418757 2219.0344
|
||||
30 202.52417 -3.4680017 0 -3.4418745 2982.7272
|
||||
40 157.39113 -3.4621782 0 -3.4418735 3631.0936
|
||||
50 126.7004 -3.4582183 0 -3.441873 4053.7725
|
||||
60 117.00722 -3.4569679 0 -3.441873 4204.9542
|
||||
70 127.65968 -3.4583427 0 -3.4418736 4106.3112
|
||||
80 151.50217 -3.4614195 0 -3.4418745 3840.7205
|
||||
90 177.67607 -3.464797 0 -3.4418754 3527.9794
|
||||
100 195.30359 -3.4670717 0 -3.4418761 3300.3795
|
||||
Loop time of 18.0803 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 0.239 ns/day, 100.446 hours/ns, 5.531 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 18.078 | 18.078 | 18.078 | 0.0 | 99.99
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.000979 | 0.000979 | 0.000979 | 0.0 | 0.01
|
||||
Output | 0.000243 | 0.000243 | 0.000243 | 0.0 | 0.00
|
||||
Modify | 0.000591 | 0.000591 | 0.000591 | 0.0 | 0.00
|
||||
Other | | 0.000469 | | | 0.00
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1959 ave 1959 max 1959 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 31232 ave 31232 max 31232 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 62464 ave 62464 max 62464 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 62464
|
||||
Ave neighs/atom = 122
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:18
|
||||
156
examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.4
Normal file
156
examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.4
Normal file
@ -0,0 +1,156 @@
|
||||
LAMMPS (2 Jun 2020)
|
||||
# Demonstrate SNAP InP potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 5.83
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a FCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice diamond $a
|
||||
lattice diamond 5.83
|
||||
Lattice spacing in x,y,z = 5.83 5.83 5.83
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
|
||||
Created 512 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass 1 114.76
|
||||
mass 2 30.98
|
||||
|
||||
# choose potential
|
||||
|
||||
include InP_JCPA2020.snap
|
||||
# DATE: 2020-06-01 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020)
|
||||
|
||||
# Definition of SNAP+ZBL potential.
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.2
|
||||
variable zblz1 equal 49
|
||||
variable zblz2 equal 15
|
||||
|
||||
# Specify hybrid with SNAP and ZBL
|
||||
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
|
||||
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
|
||||
pair_style hybrid/overlay zbl 4 4.2 snap
|
||||
pair_coeff 1 1 zbl ${zblz1} ${zblz1}
|
||||
pair_coeff 1 1 zbl 49 ${zblz1}
|
||||
pair_coeff 1 1 zbl 49 49
|
||||
pair_coeff 1 2 zbl ${zblz1} ${zblz2}
|
||||
pair_coeff 1 2 zbl 49 ${zblz2}
|
||||
pair_coeff 1 2 zbl 49 15
|
||||
pair_coeff 2 2 zbl ${zblz2} ${zblz2}
|
||||
pair_coeff 2 2 zbl 15 ${zblz2}
|
||||
pair_coeff 2 2 zbl 15 15
|
||||
pair_coeff * * snap InP_JCPA2020.snapcoeff InP_JCPA2020.snapparam In P
|
||||
Reading potential file InP_JCPA2020.snapcoeff with DATE: 2020-06-01
|
||||
SNAP Element = In, Radius 3.81205, Weight 1
|
||||
SNAP Element = P, Radius 3.82945, Weight 0.929316
|
||||
Reading potential file InP_JCPA2020.snapparam with DATE: 2020-06-01
|
||||
SNAP keyword rcutfac 1.0
|
||||
SNAP keyword twojmax 6
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0.0
|
||||
SNAP keyword bzeroflag 1
|
||||
SNAP keyword quadraticflag 0
|
||||
SNAP keyword wselfallflag 1
|
||||
SNAP keyword chemflag 1
|
||||
SNAP keyword bnormflag 1
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
|
||||
timestep 0.5e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.6589
|
||||
ghost atom cutoff = 8.6589
|
||||
binsize = 4.32945, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair zbl, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair snap, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.587 | 4.587 | 4.587 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -3.4805794 0 -3.4418771 1353.5968
|
||||
10 286.58246 -3.478848 0 -3.4418767 1582.995
|
||||
20 250.70996 -3.4742192 0 -3.4418757 2207.7507
|
||||
30 203.58199 -3.4681382 0 -3.4418746 2968.5206
|
||||
40 158.84622 -3.462366 0 -3.4418736 3619.0285
|
||||
50 128.30488 -3.4584254 0 -3.4418731 4047.173
|
||||
60 118.40349 -3.4571481 0 -3.4418731 4203.3421
|
||||
70 128.48973 -3.4584499 0 -3.4418737 4109.0296
|
||||
80 151.54241 -3.4614247 0 -3.4418746 3847.4617
|
||||
90 176.92084 -3.4646996 0 -3.4418755 3548.7811
|
||||
100 193.9555 -3.4668978 0 -3.4418761 3342.8083
|
||||
Loop time of 4.99339 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 0.865 ns/day, 27.741 hours/ns, 20.026 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.8898 | 4.907 | 4.9329 | 0.8 | 98.27
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.058815 | 0.084739 | 0.1019 | 6.1 | 1.70
|
||||
Output | 0.000252 | 0.00038775 | 0.000777 | 0.0 | 0.01
|
||||
Modify | 0.000262 | 0.00026675 | 0.000272 | 0.0 | 0.01
|
||||
Other | | 0.001039 | | | 0.02
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1099 ave 1099 max 1099 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7808 ave 7808 max 7808 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 15616 ave 15616 max 15616 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 62464
|
||||
Ave neighs/atom = 122
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:05
|
||||
18
potentials/InP_JCPA2020.snap
Normal file
18
potentials/InP_JCPA2020.snap
Normal file
@ -0,0 +1,18 @@
|
||||
# DATE: 2020-06-01 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020)
|
||||
|
||||
# Definition of SNAP+ZBL potential.
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.2
|
||||
variable zblz1 equal 49
|
||||
variable zblz2 equal 15
|
||||
|
||||
# Specify hybrid with SNAP and ZBL
|
||||
|
||||
pair_style hybrid/overlay &
|
||||
zbl ${zblcutinner} ${zblcutouter} &
|
||||
snap
|
||||
pair_coeff 1 1 zbl ${zblz1} ${zblz1}
|
||||
pair_coeff 1 2 zbl ${zblz1} ${zblz2}
|
||||
pair_coeff 2 2 zbl ${zblz2} ${zblz2}
|
||||
pair_coeff * * snap InP_JCPA2020.snapcoeff InP_JCPA2020.snapparam In P
|
||||
@ -1,4 +1,4 @@
|
||||
# LAMMPS SNAP coefficients for InP
|
||||
# DATE: 2020-06-01 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020)
|
||||
|
||||
2 241
|
||||
In 3.81205 1
|
||||
15
potentials/InP_JCPA2020.snapparam
Normal file
15
potentials/InP_JCPA2020.snapparam
Normal file
@ -0,0 +1,15 @@
|
||||
# DATE: 2020-06-01 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020)
|
||||
|
||||
# required
|
||||
rcutfac 1.0
|
||||
twojmax 6
|
||||
|
||||
# optional
|
||||
rfac0 0.99363
|
||||
rmin0 0.0
|
||||
bzeroflag 1
|
||||
quadraticflag 0
|
||||
wselfallflag 1
|
||||
chemflag 1
|
||||
bnormflag 1
|
||||
|
||||
@ -515,7 +515,7 @@ void PairSNAPKokkos<DeviceType>::coeff(int narg, char **arg)
|
||||
Kokkos::deep_copy(d_map,h_map);
|
||||
|
||||
snaKK = SNAKokkos<DeviceType>(rfac0,twojmax,
|
||||
rmin0,switchflag,bzeroflag,alloyflag,wselfallflag,nelements);
|
||||
rmin0,switchflag,bzeroflag,chemflag,bnormflag,wselfallflag,nelements);
|
||||
snaKK.grow_rij(0,0);
|
||||
snaKK.init();
|
||||
}
|
||||
@ -584,7 +584,7 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeNeigh,const typen
|
||||
my_sna.inside(ii,offset) = j;
|
||||
my_sna.wj(ii,offset) = d_wjelem[elem_j];
|
||||
my_sna.rcutij(ii,offset) = (radi + d_radelem[elem_j])*rcutfac;
|
||||
if (alloyflag)
|
||||
if (chemflag)
|
||||
my_sna.element(ii,offset) = elem_j;
|
||||
else
|
||||
my_sna.element(ii,offset) = 0;
|
||||
|
||||
@ -210,7 +210,7 @@ inline
|
||||
int switch_flag;
|
||||
|
||||
// Chem snap flags
|
||||
int alloy_flag;
|
||||
int chem_flag;
|
||||
int bnorm_flag;
|
||||
int nelements;
|
||||
int ndoubles;
|
||||
|
||||
@ -29,7 +29,7 @@ template<class DeviceType>
|
||||
inline
|
||||
SNAKokkos<DeviceType>::SNAKokkos(double rfac0_in,
|
||||
int twojmax_in, double rmin0_in, int switch_flag_in, int bzero_flag_in,
|
||||
int alloy_flag_in, int wselfall_flag_in, int nelements_in)
|
||||
int chem_flag_in, int bnorm_flag_in, int wselfall_flag_in, int nelements_in)
|
||||
{
|
||||
wself = 1.0;
|
||||
|
||||
@ -38,13 +38,13 @@ SNAKokkos<DeviceType>::SNAKokkos(double rfac0_in,
|
||||
switch_flag = switch_flag_in;
|
||||
bzero_flag = bzero_flag_in;
|
||||
|
||||
alloy_flag = alloy_flag_in;
|
||||
wselfall_flag = wselfall_flag_in;
|
||||
if (alloy_flag)
|
||||
chem_flag = chem_flag_in;
|
||||
if (chem_flag)
|
||||
nelements = nelements_in;
|
||||
else
|
||||
nelements = 1;
|
||||
bnorm_flag = alloy_flag_in;
|
||||
bnorm_flag = bnorm_flag_in;
|
||||
wselfall_flag = wselfall_flag_in;
|
||||
|
||||
twojmax = twojmax_in;
|
||||
|
||||
@ -283,7 +283,7 @@ 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
|
||||
SNAcomplex init = {0., 0.};
|
||||
if (m % (j+2) == 0 && (!alloy_flag || ielem == jelem || wselfall_flag)) { init = {wself, 0.0}; } //need to map iatom to element
|
||||
if (m % (j+2) == 0 && (!chem_flag || ielem == jelem || wselfall_flag)) { init = {wself, 0.0}; } //need to map iatom to element
|
||||
|
||||
ulisttot(jelem*idxu_max+jjup, iatom) = init;
|
||||
});
|
||||
@ -1620,7 +1620,7 @@ int SNAKokkos<DeviceType>::compute_ncoeff()
|
||||
|
||||
ndoubles = nelements*nelements;
|
||||
ntriples = nelements*nelements*nelements;
|
||||
if (alloy_flag) ncount *= ntriples;
|
||||
if (chem_flag) ncount *= ntriples;
|
||||
|
||||
return ncount;
|
||||
}
|
||||
|
||||
@ -34,7 +34,7 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
radelem(NULL), wjelem(NULL)
|
||||
{
|
||||
double rmin0, rfac0;
|
||||
int twojmax, switchflag, bzeroflag, bnormflag;
|
||||
int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
|
||||
radelem = NULL;
|
||||
wjelem = NULL;
|
||||
|
||||
@ -50,7 +50,8 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
bzeroflag = 1;
|
||||
bnormflag = 0;
|
||||
quadraticflag = 0;
|
||||
alloyflag = 0;
|
||||
chemflag = 0;
|
||||
bnormflag = 0;
|
||||
wselfallflag = 0;
|
||||
nelements = 1;
|
||||
|
||||
@ -108,22 +109,25 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
error->all(FLERR,"Illegal compute sna/atom command");
|
||||
quadraticflag = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"alloy") == 0) {
|
||||
} else if (strcmp(arg[iarg],"chem") == 0) {
|
||||
if (iarg+2+ntypes > narg)
|
||||
error->all(FLERR,"Illegal compute sna/atom command");
|
||||
alloyflag = 1;
|
||||
bnormflag = alloyflag;
|
||||
chemflag = 1;
|
||||
memory->create(map,ntypes+1,"compute_sna_atom:map");
|
||||
nelements = force->inumeric(FLERR,arg[iarg+1]);
|
||||
for(int i = 0; i < ntypes; i++) {
|
||||
int jelem = force->inumeric(FLERR,arg[iarg+2+i]);
|
||||
printf("%d %d %d %d\n",ntypes,nelements,i,jelem);
|
||||
if (jelem < 0 || jelem >= nelements)
|
||||
error->all(FLERR,"Illegal compute sna/atom command");
|
||||
map[i+1] = jelem;
|
||||
}
|
||||
iarg += 2+ntypes;
|
||||
} else if (strcmp(arg[iarg],"wselfall") == 0) {
|
||||
} else if (strcmp(arg[iarg],"bnormflag") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute sna/atom command");
|
||||
bnormflag = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"wselfallflag") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute sna/atom command");
|
||||
wselfallflag = atoi(arg[iarg+1]);
|
||||
@ -133,7 +137,7 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
snaptr = new SNA(lmp, rfac0, twojmax,
|
||||
rmin0, switchflag, bzeroflag,
|
||||
alloyflag, wselfallflag, nelements);
|
||||
chemflag, bnormflag, wselfallflag, nelements);
|
||||
|
||||
ncoeff = snaptr->ncoeff;
|
||||
size_peratom_cols = ncoeff;
|
||||
@ -229,7 +233,7 @@ void ComputeSNAAtom::compute_peratom()
|
||||
const double ztmp = x[i][2];
|
||||
const int itype = type[i];
|
||||
int ielem = 0;
|
||||
if (alloyflag)
|
||||
if (chemflag)
|
||||
ielem = map[itype];
|
||||
const double radi = radelem[itype];
|
||||
const int* const jlist = firstneigh[i];
|
||||
@ -254,7 +258,7 @@ void ComputeSNAAtom::compute_peratom()
|
||||
const double rsq = delx*delx + dely*dely + delz*delz;
|
||||
int jtype = type[j];
|
||||
int jelem = 0;
|
||||
if (alloyflag)
|
||||
if (chemflag)
|
||||
int jelem = map[jtype];
|
||||
if (rsq < cutsq[itype][jtype] && rsq>1e-20) {
|
||||
snaptr->rij[ninside][0] = delx;
|
||||
|
||||
@ -43,7 +43,7 @@ class ComputeSNAAtom : public Compute {
|
||||
double *radelem;
|
||||
double *wjelem;
|
||||
int * map; // map types to [0,nelements)
|
||||
int nelements, alloyflag, wselfallflag;
|
||||
int nelements, chemflag;
|
||||
class SNA* snaptr;
|
||||
double cutmax;
|
||||
int quadraticflag;
|
||||
|
||||
@ -34,7 +34,7 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
radelem(NULL), wjelem(NULL)
|
||||
{
|
||||
double rfac0, rmin0;
|
||||
int twojmax, switchflag, bzeroflag, bnormflag;
|
||||
int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
|
||||
radelem = NULL;
|
||||
wjelem = NULL;
|
||||
|
||||
@ -50,7 +50,8 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
bzeroflag = 1;
|
||||
bnormflag = 0;
|
||||
quadraticflag = 0;
|
||||
alloyflag = 0;
|
||||
chemflag = 0;
|
||||
bnormflag = 0;
|
||||
wselfallflag = 0;
|
||||
nelements = 1;
|
||||
|
||||
@ -106,22 +107,25 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
error->all(FLERR,"Illegal compute snad/atom command");
|
||||
quadraticflag = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"alloy") == 0) {
|
||||
} else if (strcmp(arg[iarg],"chem") == 0) {
|
||||
if (iarg+2+ntypes > narg)
|
||||
error->all(FLERR,"Illegal compute snad/atom command");
|
||||
alloyflag = 1;
|
||||
bnormflag = alloyflag;
|
||||
chemflag = 1;
|
||||
memory->create(map,ntypes+1,"compute_snad_atom:map");
|
||||
nelements = force->inumeric(FLERR,arg[iarg+1]);
|
||||
for(int i = 0; i < ntypes; i++) {
|
||||
int jelem = force->inumeric(FLERR,arg[iarg+2+i]);
|
||||
printf("%d %d %d %d\n",ntypes,nelements,i,jelem);
|
||||
if (jelem < 0 || jelem >= nelements)
|
||||
error->all(FLERR,"Illegal compute snad/atom command");
|
||||
map[i+1] = jelem;
|
||||
}
|
||||
iarg += 2+ntypes;
|
||||
} else if (strcmp(arg[iarg],"wselfall") == 0) {
|
||||
} else if (strcmp(arg[iarg],"bnormflag") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute snad/atom command");
|
||||
bnormflag = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"wselfallflag") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute snad/atom command");
|
||||
wselfallflag = atoi(arg[iarg+1]);
|
||||
@ -131,7 +135,7 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
snaptr = new SNA(lmp, rfac0, twojmax,
|
||||
rmin0, switchflag, bzeroflag,
|
||||
alloyflag, wselfallflag, nelements);
|
||||
chemflag, bnormflag, wselfallflag, nelements);
|
||||
|
||||
ncoeff = snaptr->ncoeff;
|
||||
nperdim = ncoeff;
|
||||
@ -241,7 +245,7 @@ void ComputeSNADAtom::compute_peratom()
|
||||
const double ztmp = x[i][2];
|
||||
const int itype = type[i];
|
||||
int ielem = 0;
|
||||
if (alloyflag)
|
||||
if (chemflag)
|
||||
ielem = map[itype];
|
||||
const double radi = radelem[itype];
|
||||
const int* const jlist = firstneigh[i];
|
||||
@ -272,7 +276,7 @@ void ComputeSNADAtom::compute_peratom()
|
||||
const double rsq = delx*delx + dely*dely + delz*delz;
|
||||
int jtype = type[j];
|
||||
int jelem = 0;
|
||||
if (alloyflag)
|
||||
if (chemflag)
|
||||
jelem = map[jtype];
|
||||
if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
|
||||
snaptr->rij[ninside][0] = delx;
|
||||
|
||||
@ -45,7 +45,7 @@ class ComputeSNADAtom : public Compute {
|
||||
double *radelem;
|
||||
double *wjelem;
|
||||
int *map; // map types to [0,nelements)
|
||||
int nelements, alloyflag, wselfallflag;
|
||||
int nelements, chemflag;
|
||||
class SNA* snaptr;
|
||||
double cutmax;
|
||||
int quadraticflag;
|
||||
|
||||
@ -41,7 +41,7 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
|
||||
extarray = 0;
|
||||
|
||||
double rfac0, rmin0;
|
||||
int twojmax, switchflag, bzeroflag;
|
||||
int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
|
||||
radelem = NULL;
|
||||
wjelem = NULL;
|
||||
|
||||
@ -56,7 +56,8 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
|
||||
switchflag = 1;
|
||||
bzeroflag = 1;
|
||||
quadraticflag = 0;
|
||||
alloyflag = 0;
|
||||
chemflag = 0;
|
||||
bnormflag = 0;
|
||||
wselfallflag = 0;
|
||||
nelements = 1;
|
||||
|
||||
@ -112,20 +113,24 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
|
||||
error->all(FLERR,"Illegal compute snap command");
|
||||
quadraticflag = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"alloyflag") == 0) {
|
||||
} else if (strcmp(arg[iarg],"chem") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute snap command");
|
||||
alloyflag = 1;
|
||||
chemflag = 1;
|
||||
memory->create(map,ntypes+1,"compute_snap:map");
|
||||
nelements = force->inumeric(FLERR,arg[iarg+1]);
|
||||
for(int i = 0; i < ntypes; i++) {
|
||||
int jelem = force->inumeric(FLERR,arg[iarg+2+i]);
|
||||
if (screen && comm->me==0) fprintf(screen, "%d %d %d %d\n",ntypes,nelements,i,jelem);
|
||||
if (jelem < 0 || jelem >= nelements)
|
||||
error->all(FLERR,"Illegal compute snap command");
|
||||
map[i+1] = jelem;
|
||||
}
|
||||
iarg += 2+ntypes;
|
||||
} else if (strcmp(arg[iarg],"bnormflag") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute snap command");
|
||||
bnormflag = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"wselfallflag") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute snap command");
|
||||
@ -136,7 +141,7 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
snaptr = new SNA(lmp, rfac0, twojmax,
|
||||
rmin0, switchflag, bzeroflag,
|
||||
alloyflag, wselfallflag, nelements);
|
||||
chemflag, bnormflag, wselfallflag, nelements);
|
||||
|
||||
ncoeff = snaptr->ncoeff;
|
||||
nperdim = ncoeff;
|
||||
@ -168,7 +173,7 @@ ComputeSnap::~ComputeSnap()
|
||||
memory->destroy(cutsq);
|
||||
delete snaptr;
|
||||
|
||||
if (alloyflag) memory->destroy(map);
|
||||
if (chemflag) memory->destroy(map);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -300,7 +305,7 @@ void ComputeSnap::compute_array()
|
||||
const double ztmp = x[i][2];
|
||||
const int itype = type[i];
|
||||
int ielem = 0;
|
||||
if (alloyflag)
|
||||
if (chemflag)
|
||||
ielem = map[itype];
|
||||
const double radi = radelem[itype];
|
||||
const int* const jlist = firstneigh[i];
|
||||
@ -328,7 +333,7 @@ void ComputeSnap::compute_array()
|
||||
const double rsq = delx*delx + dely*dely + delz*delz;
|
||||
int jtype = type[j];
|
||||
int jelem = 0;
|
||||
if (alloyflag)
|
||||
if (chemflag)
|
||||
jelem = map[jtype];
|
||||
if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
|
||||
snaptr->rij[ninside][0] = delx;
|
||||
|
||||
@ -45,7 +45,7 @@ class ComputeSnap : public Compute {
|
||||
double *radelem;
|
||||
double *wjelem;
|
||||
int *map; // map types to [0,nelements)
|
||||
int nelements, alloyflag, wselfallflag;
|
||||
int nelements, chemflag;
|
||||
class SNA* snaptr;
|
||||
double cutmax;
|
||||
int quadraticflag;
|
||||
|
||||
@ -33,7 +33,7 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
radelem(NULL), wjelem(NULL)
|
||||
{
|
||||
double rfac0, rmin0;
|
||||
int twojmax, switchflag, bzeroflag, bnormflag;
|
||||
int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
|
||||
radelem = NULL;
|
||||
wjelem = NULL;
|
||||
|
||||
@ -49,7 +49,8 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
bzeroflag = 1;
|
||||
bnormflag = 0;
|
||||
quadraticflag = 0;
|
||||
alloyflag = 0;
|
||||
chemflag = 0;
|
||||
bnormflag = 0;
|
||||
wselfallflag = 0;
|
||||
nelements = 1;
|
||||
|
||||
@ -101,22 +102,25 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
error->all(FLERR,"Illegal compute snav/atom command");
|
||||
quadraticflag = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"alloy") == 0) {
|
||||
} else if (strcmp(arg[iarg],"chem") == 0) {
|
||||
if (iarg+2+ntypes > narg)
|
||||
error->all(FLERR,"Illegal compute sna/atom command");
|
||||
alloyflag = 1;
|
||||
bnormflag = alloyflag;
|
||||
chemflag = 1;
|
||||
memory->create(map,ntypes+1,"compute_sna_atom:map");
|
||||
nelements = force->inumeric(FLERR,arg[iarg+1]);
|
||||
for(int i = 0; i < ntypes; i++) {
|
||||
int jelem = force->inumeric(FLERR,arg[iarg+2+i]);
|
||||
printf("%d %d %d %d\n",ntypes,nelements,i,jelem);
|
||||
if (jelem < 0 || jelem >= nelements)
|
||||
error->all(FLERR,"Illegal compute snav/atom command");
|
||||
map[i+1] = jelem;
|
||||
}
|
||||
iarg += 2+ntypes;
|
||||
} else if (strcmp(arg[iarg],"wselfall") == 0) {
|
||||
} else if (strcmp(arg[iarg],"bnormflag") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute snav/atom command");
|
||||
bnormflag = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"wselfallflag") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute snav/atom command");
|
||||
wselfallflag = atoi(arg[iarg+1]);
|
||||
@ -126,7 +130,7 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
snaptr = new SNA(lmp, rfac0, twojmax,
|
||||
rmin0, switchflag, bzeroflag,
|
||||
alloyflag, wselfallflag, nelements);
|
||||
chemflag, bnormflag, wselfallflag, nelements);
|
||||
|
||||
ncoeff = snaptr->ncoeff;
|
||||
nperdim = ncoeff;
|
||||
@ -236,7 +240,7 @@ void ComputeSNAVAtom::compute_peratom()
|
||||
const double ztmp = x[i][2];
|
||||
const int itype = type[i];
|
||||
int ielem = 0;
|
||||
if (alloyflag)
|
||||
if (chemflag)
|
||||
ielem = map[itype];
|
||||
const double radi = radelem[itype];
|
||||
|
||||
@ -265,7 +269,7 @@ void ComputeSNAVAtom::compute_peratom()
|
||||
const double rsq = delx*delx + dely*dely + delz*delz;
|
||||
int jtype = type[j];
|
||||
int jelem = 0;
|
||||
if (alloyflag)
|
||||
if (chemflag)
|
||||
jelem = map[jtype];
|
||||
if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
|
||||
snaptr->rij[ninside][0] = delx;
|
||||
|
||||
@ -45,7 +45,7 @@ class ComputeSNAVAtom : public Compute {
|
||||
double *radelem;
|
||||
double *wjelem;
|
||||
int *map; // map types to [0,nelements)
|
||||
int nelements, alloyflag, wselfallflag;
|
||||
int nelements, chemflag;
|
||||
class SNA* snaptr;
|
||||
int quadraticflag;
|
||||
};
|
||||
|
||||
@ -156,14 +156,14 @@ void PairSNAP::compute(int eflag, int vflag)
|
||||
snaptr->inside[ninside] = j;
|
||||
snaptr->wj[ninside] = wjelem[jelem];
|
||||
snaptr->rcutij[ninside] = (radi + radelem[jelem])*rcutfac;
|
||||
snaptr->element[ninside] = jelem; // element index for alloy snap
|
||||
snaptr->element[ninside] = jelem;
|
||||
ninside++;
|
||||
}
|
||||
}
|
||||
|
||||
// compute Ui, Yi for atom I
|
||||
|
||||
if (alloyflag)
|
||||
if (chemflag)
|
||||
snaptr->compute_ui(ninside, ielem);
|
||||
else
|
||||
snaptr->compute_ui(ninside, 0);
|
||||
@ -176,7 +176,7 @@ void PairSNAP::compute(int eflag, int vflag)
|
||||
|
||||
for (int jj = 0; jj < ninside; jj++) {
|
||||
int j = snaptr->inside[jj];
|
||||
if(alloyflag)
|
||||
if(chemflag)
|
||||
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
|
||||
snaptr->rcutij[jj],jj, snaptr->element[jj]);
|
||||
else
|
||||
@ -328,17 +328,17 @@ void PairSNAP::compute_bispectrum()
|
||||
snaptr->inside[ninside] = j;
|
||||
snaptr->wj[ninside] = wjelem[jelem];
|
||||
snaptr->rcutij[ninside] = (radi + radelem[jelem])*rcutfac;
|
||||
snaptr->element[ninside] = jelem; // element index for alloy snap
|
||||
snaptr->element[ninside] = jelem;
|
||||
ninside++;
|
||||
}
|
||||
}
|
||||
|
||||
if (alloyflag)
|
||||
if (chemflag)
|
||||
snaptr->compute_ui(ninside, ielem);
|
||||
else
|
||||
snaptr->compute_ui(ninside, 0);
|
||||
snaptr->compute_zi();
|
||||
if (alloyflag)
|
||||
if (chemflag)
|
||||
snaptr->compute_bi(ielem);
|
||||
else
|
||||
snaptr->compute_bi(0);
|
||||
@ -418,7 +418,6 @@ void PairSNAP::coeff(int narg, char **arg)
|
||||
ncoeffq = (ncoeff*(ncoeff+1))/2;
|
||||
int ntmp = 1+ncoeff+ncoeffq;
|
||||
if (ntmp != ncoeffall) {
|
||||
printf("ncoeffall = %d ntmp = %d ncoeff = %d \n",ncoeffall,ntmp,ncoeff);
|
||||
error->all(FLERR,"Incorrect SNAP coeff file");
|
||||
}
|
||||
}
|
||||
@ -461,7 +460,7 @@ void PairSNAP::coeff(int narg, char **arg)
|
||||
|
||||
snaptr = new SNA(lmp, rfac0, twojmax,
|
||||
rmin0, switchflag, bzeroflag,
|
||||
alloyflag, wselfallflag, nelements);
|
||||
chemflag, bnormflag, wselfallflag, nelements);
|
||||
|
||||
if (ncoeff != snaptr->ncoeff) {
|
||||
if (comm->me == 0)
|
||||
@ -653,9 +652,9 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
|
||||
rmin0 = 0.0;
|
||||
switchflag = 1;
|
||||
bzeroflag = 1;
|
||||
bnormflag = 0;
|
||||
quadraticflag = 0;
|
||||
alloyflag = 0;
|
||||
chemflag = 0;
|
||||
bnormflag = 0;
|
||||
wselfallflag = 0;
|
||||
chunksize = 2000;
|
||||
|
||||
@ -721,8 +720,10 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
|
||||
bzeroflag = atoi(keyval);
|
||||
else if (strcmp(keywd,"quadraticflag") == 0)
|
||||
quadraticflag = atoi(keyval);
|
||||
else if (strcmp(keywd,"alloyflag") == 0)
|
||||
alloyflag = atoi(keyval);
|
||||
else if (strcmp(keywd,"chemflag") == 0)
|
||||
chemflag = atoi(keyval);
|
||||
else if (strcmp(keywd,"bnormflag") == 0)
|
||||
bnormflag = atoi(keyval);
|
||||
else if (strcmp(keywd,"wselfallflag") == 0)
|
||||
wselfallflag = atoi(keyval);
|
||||
else if (strcmp(keywd,"chunksize") == 0)
|
||||
@ -731,8 +732,6 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
|
||||
error->all(FLERR,"Incorrect SNAP parameter file");
|
||||
}
|
||||
|
||||
bnormflag = alloyflag;
|
||||
|
||||
if (rcutfacflag == 0 || twojmaxflag == 0)
|
||||
error->all(FLERR,"Incorrect SNAP parameter file");
|
||||
|
||||
|
||||
@ -59,7 +59,7 @@ protected:
|
||||
double** bispectrum; // bispectrum components for all atoms in list
|
||||
int *map; // mapping from atom types to elements
|
||||
int twojmax, switchflag, bzeroflag, bnormflag;
|
||||
int alloyflag, wselfallflag;
|
||||
int chemflag, wselfallflag;
|
||||
int chunksize;
|
||||
double rfac0, rmin0, wj1, wj2;
|
||||
int rcutfacflag, twojmaxflag; // flags for required parameters
|
||||
|
||||
@ -109,7 +109,7 @@ using namespace MathConst;
|
||||
|
||||
SNA::SNA(LAMMPS* lmp, double rfac0_in, int twojmax_in,
|
||||
double rmin0_in, int switch_flag_in, int bzero_flag_in,
|
||||
int alloy_flag_in, int wselfall_flag_in, int nelements_in) : Pointers(lmp)
|
||||
int chem_flag_in, int bnorm_flag_in, int wselfall_flag_in, int nelements_in) : Pointers(lmp)
|
||||
{
|
||||
wself = 1.0;
|
||||
|
||||
@ -117,11 +117,15 @@ SNA::SNA(LAMMPS* lmp, double rfac0_in, int twojmax_in,
|
||||
rmin0 = rmin0_in;
|
||||
switch_flag = switch_flag_in;
|
||||
bzero_flag = bzero_flag_in;
|
||||
bnorm_flag = alloy_flag_in;
|
||||
alloy_flag = alloy_flag_in;
|
||||
chem_flag = chem_flag_in;
|
||||
bnorm_flag = bnorm_flag_in;
|
||||
wselfall_flag = wselfall_flag_in;
|
||||
|
||||
if (alloy_flag)
|
||||
if (bnorm_flag != chem_flag)
|
||||
lmp->error->warning(FLERR, "bnormflag and chemflag are not equal."
|
||||
"This is probably not what you intended");
|
||||
|
||||
if (chem_flag)
|
||||
nelements = nelements_in;
|
||||
else
|
||||
nelements = 1;
|
||||
@ -351,7 +355,7 @@ void SNA::compute_ui(int jnum, int ielem)
|
||||
z0 = r / tan(theta0);
|
||||
|
||||
compute_uarray(x, y, z, z0, r, j);
|
||||
if (alloy_flag)
|
||||
if (chem_flag)
|
||||
add_uarraytot(r, wj[j], rcutij[j], j, element[j]);
|
||||
else
|
||||
add_uarraytot(r, wj[j], rcutij[j], j, 0);
|
||||
@ -1688,7 +1692,7 @@ void SNA::compute_ncoeff()
|
||||
|
||||
ndoubles = nelements*nelements;
|
||||
ntriples = nelements*nelements*nelements;
|
||||
if (alloy_flag)
|
||||
if (chem_flag)
|
||||
ncoeff = ncount*ntriples;
|
||||
else
|
||||
ncoeff = ncount;
|
||||
|
||||
@ -33,7 +33,7 @@ struct SNA_BINDICES {
|
||||
class SNA : protected Pointers {
|
||||
|
||||
public:
|
||||
SNA(LAMMPS*, double, int, double, int, int, int, int, int);
|
||||
SNA(LAMMPS*, double, int, double, int, int, int, int, int, int);
|
||||
|
||||
SNA(LAMMPS* lmp) : Pointers(lmp) {};
|
||||
~SNA();
|
||||
@ -129,7 +129,7 @@ private:
|
||||
int bzero_flag; // 1 if bzero subtracted from barray
|
||||
double* bzero; // array of B values for isolated atoms
|
||||
int bnorm_flag; // 1 if barray divided by j+1
|
||||
int alloy_flag; // 1 for multi-element bispectrum components
|
||||
int chem_flag; // 1 for multi-element bispectrum components
|
||||
int wselfall_flag; // 1 for adding wself to all element labelings
|
||||
int nelements; // number of elements
|
||||
int ndoubles; // number of multi-element pairs
|
||||
|
||||
Reference in New Issue
Block a user