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Merge branch 'DOI' of github.com:e-kwsm/lammps into doc-cleanup

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Axel Kohlmeyer
2020-03-12 05:43:44 -04:00
parent 23a402ddd3 8af9d40392
commit 1372c20d94
37 changed files with 89 additions and 94 deletions
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4
cmake/README.md
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@ -1383,8 +1383,8 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
Some potentials that are also implemented in the Yet Another Force Field (YAFF) code. Some potentials that are also implemented in the Yet Another Force Field (YAFF) code.
The expressions and their use are discussed in the following papers: The expressions and their use are discussed in the following papers:
<ul> <ul>
<li><a href="http://dx.doi.org/10.1002/jcc.23877" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015)</a></li> <li><a href="https://doi.org/10.1002/jcc.23877" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015)</a></li>
<li><a href="http://dx.doi.org/10.1002/jcc.25173" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018)</a></li> <li><a href="https://doi.org/10.1002/jcc.25173" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018)</a></li>
</ul> </ul>
</td> </td>
<td> <td>

6
cmake/presets/all_off.cmake
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@ -7,11 +7,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
SRD VORONOI SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
USER-TALLY USER-UEF USER-VTK USER-YAFF) USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES}) foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE) set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

6
cmake/presets/all_on.cmake
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@ -9,11 +9,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
SRD VORONOI SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
USER-TALLY USER-UEF USER-VTK USER-YAFF) USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES}) foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE) set(PKG_${PKG} ON CACHE BOOL "" FORCE)

14
cmake/presets/most.cmake
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@ -2,13 +2,13 @@
# external libraries. Compared to all_on.cmake some more unusual packages # external libraries. Compared to all_on.cmake some more unusual packages
# are removed. The resulting binary should be able to run most inputs. # are removed. The resulting binary should be able to run most inputs.
set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL
GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
PYTHON QEQ REPLICA RIGID SHOCK SNAP SRD VORONOI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
USER-DRUDE USER-FEP USER-MEAMC USER-MESO USER-DPD USER-DRUDE USER-FEP USER-MEAMC USER-MESODPD
USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
USER-SPH USER-SMD USER-UEF USER-YAFF) USER-REAXC USER-SPH USER-SMD USER-UEF USER-YAFF)
foreach(PKG ${ALL_PACKAGES}) foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE) set(PKG_${PKG} ON CACHE BOOL "" FORCE)

4
doc/src/Howto_tip4p.rst
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@ -41,7 +41,7 @@ coefficients.
| |
For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005); For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
http://dx.doi.org/10.1063/1.1931662) these values can be used: https://doi.org/10.1063/1.1931662) these values can be used:
| O mass = 15.9994 | O mass = 15.9994
| H mass = 1.008 | H mass = 1.008
@ -57,7 +57,7 @@ http://dx.doi.org/10.1063/1.1931662) these values can be used:
| |
For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005); For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
http://dx.doi.org/10.1063/1.2121687), these values can be used: https://doi.org/10.1063/1.2121687), these values can be used:
| O mass = 15.9994 | O mass = 15.9994
| H mass = 1.008 | H mass = 1.008

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doc/src/Packages_details.rst
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@ -2339,8 +2339,8 @@ The expressions and their use are discussed in the following papers
which discuss the `QuickFF <quickff_>`_ methodology. which discuss the `QuickFF <quickff_>`_ methodology.
.. _vanduyfhuys2015: http://dx.doi.org/10.1002/jcc.23877 .. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877
.. _vanduyfhuys2018: http://dx.doi.org/10.1002/jcc.25173 .. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173
.. _quickff: http://molmod.github.io/QuickFF .. _quickff: http://molmod.github.io/QuickFF
.. _yaff: https://github.com/molmod/yaff .. _yaff: https://github.com/molmod/yaff

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doc/src/fix_orient.rst
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@ -193,7 +193,7 @@ Science, 117, 397-405 (2016).
.. _Wicaksono2: .. _Wicaksono2:
**(Wicaksono2)** Wicaksono, figshare, **(Wicaksono2)** Wicaksono, figshare,
https://dx.doi.org/10.6084/m9.figshare.1488628.v1 (2015). https://doi.org/10.6084/m9.figshare.1488628.v1 (2015).
---------- ----------

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doc/src/fix_phonon.rst
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@ -203,19 +203,19 @@ the :doc:`dimension <dimension>` command, and nasr = 20.
**(Campana)** C. Campana and **(Campana)** C. Campana and
M. H. Muser, *Practical Green's function approach to the M. H. Muser, *Practical Green's function approach to the
simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) <http://dx.doi.org/10.1103/PhysRevB.74.075420>`_ simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) <https://doi.org/10.1103/PhysRevB.74.075420>`_
.. _Kong: .. _Kong:
**(Kong)** L.T. Kong, G. Bartels, C. Campana, **(Kong)** L.T. Kong, G. Bartels, C. Campana,
C. Denniston, and Martin H. Muser, *Implementation of Green's C. Denniston, and Martin H. Muser, *Implementation of Green's
function molecular dynamics: An extension to LAMMPS*\ , `Computer Physics Communications [180](6):1004-1010 (2009). <http://dx.doi.org/10.1016/j.cpc.2008.12.035>`_ function molecular dynamics: An extension to LAMMPS*\ , `Computer Physics Communications [180](6):1004-1010 (2009). <https://doi.org/10.1016/j.cpc.2008.12.035>`_
L.T. Kong, C. Denniston, and Martin H. Muser, L.T. Kong, C. Denniston, and Martin H. Muser,
*An improved version of the Green's function molecular dynamics *An improved version of the Green's function molecular dynamics
method*\ , `Computer Physics Communications [182](2):540-541 (2011). <http://dx.doi.org/10.1016/j.cpc.2010.10.006>`_ method*\ , `Computer Physics Communications [182](2):540-541 (2011). <https://doi.org/10.1016/j.cpc.2010.10.006>`_
.. _Kong2011: .. _Kong2011:
**(Kong2011)** L.T. Kong, *Phonon dispersion measured directly from **(Kong2011)** L.T. Kong, *Phonon dispersion measured directly from
molecular dynamics simulations*\ , `Computer Physics Communications [182](10):2201-2207, (2011). <http://dx.doi.org/10.1016/j.cpc.2011.04.019>`_ molecular dynamics simulations*\ , `Computer Physics Communications [182](10):2201-2207, (2011). <https://doi.org/10.1016/j.cpc.2011.04.019>`_

2
doc/src/fix_poems.rst
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@ -140,4 +140,4 @@ Related commands
**(Anderson)** Anderson, Mukherjee, Critchley, Ziegler, and Lipton **(Anderson)** Anderson, Mukherjee, Critchley, Ziegler, and Lipton
"POEMS: Parallelizable Open-source Efficient Multibody Software ", "POEMS: Parallelizable Open-source Efficient Multibody Software ",
Engineering With Computers (2006). (`link to paper <http://dx.doi.org/10.1007/s00366-006-0026-x>`_) Engineering With Computers (2006). (`link to paper <https://doi.org/10.1007/s00366-006-0026-x>`_)

9
doc/src/pair_dpd.rst
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@ -126,9 +126,14 @@ the work of :ref:`(Afshar) <Afshar>` and :ref:`(Phillips) <Phillips>`.
.. note:: .. note::
The virial calculation for pressure when using this pair style The virial calculation for pressure when using these pair styles
includes all the components of force listed above, including the includes all the components of force listed above, including the
random force. random force. Since the random force depends on random numbers,
everything that changes the order of atoms in the neighbor list
(e.g. different number of MPI ranks or a different neighbor list
skin distance) will also change the sequence in which the random
numbers are applied and thus the individual forces and therefore
also the virial/pressure.
---------- ----------

12
doc/src/pair_srp.rst
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@ -15,9 +15,9 @@ Syntax
* distance = *min* or *mid* * distance = *min* or *mid*
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *exclude* * keyword = *exclude*
.. parsed-literal:: .. parsed-literal::
*bptype* value = atom type for bond particles *bptype* value = atom type for bond particles
*exclude* value = *yes* or *no* *exclude* value = *yes* or *no*
@ -31,7 +31,7 @@ Examples
pair_coeff 1 2 none pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8 pair_coeff 2 2 srp 100.0 0.8
pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 \* min exclude yes pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
pair_coeff 1 1 dpd 60.0 50 1.0 pair_coeff 1 1 dpd 60.0 50 1.0
pair_coeff 1 2 none pair_coeff 1 2 none
pair_coeff 2 2 srp 40.0 pair_coeff 2 2 srp 40.0
@ -57,7 +57,7 @@ bond-pairwise potential, such that the force on bond *i* due to bond
.. math:: .. math::
F^{SRP}_{ij} & = C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c F^{\mathrm{SRP}}_{ij} = C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c
where *r* and :math:`\hat{r}_{ij}` are the distance and unit vector where *r* and :math:`\hat{r}_{ij}` are the distance and unit vector
between the two bonds. Note that *btype* can be specified as an between the two bonds. Note that *btype* can be specified as an
@ -70,8 +70,8 @@ lever rule,
.. math:: .. math::
F_{i1}^{SRP} & = F^{SRP}_{ij}(L) \\ F_{i1}^{\mathrm{SRP}} & = F^{\mathrm{SRP}}_{ij}(L) \\
F_{i2}^{SRP} & = F^{SRP}_{ij}(1-L) F_{i2}^{\mathrm{SRP}} & = F^{\mathrm{SRP}}_{ij}(1-L)
where *L* is the normalized distance from the atom to the point of where *L* is the normalized distance from the atom to the point of
closest approach of bond *i* and *j*\ . The *mid* option takes *L* as closest approach of bond *i* and *j*\ . The *mid* option takes *L* as

2
examples/HEAT/README
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@ -6,7 +6,7 @@ All input scripts are part of the supplementary (open access) material
supporting the publication of Wirnsberger et al. [J. Chem. Phys. 143, supporting the publication of Wirnsberger et al. [J. Chem. Phys. 143,
124104 (2015)] and allow one to reproduce the key results reported in 124104 (2015)] and allow one to reproduce the key results reported in
that paper. The full article is available for download under that paper. The full article is available for download under
http://dx.doi.org/10.1063/1.4931597 or http://arxiv.org/pdf/1507.07081 https://doi.org/10.1063/1.4931597 or http://arxiv.org/pdf/1507.07081
and the supplementary material is available under and the supplementary material is available under
https://www.repository.cam.ac.uk/handle/1810/250539. https://www.repository.cam.ac.uk/handle/1810/250539.

4
examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1
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@ -101,7 +101,7 @@ colvars: Creating proxy instance
colvars: ---------------------------------------------------------------------- colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16. colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013: colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594 colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation. colvars: in any publication based on this calculation.
colvars: SMP parallelism is available. colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29. colvars: Using LAMMPS interface, version 2018-08-29.
@ -405,7 +405,7 @@ colvars: Creating proxy instance
colvars: ---------------------------------------------------------------------- colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16. colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013: colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594 colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation. colvars: in any publication based on this calculation.
colvars: SMP parallelism is available. colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29. colvars: Using LAMMPS interface, version 2018-08-29.

4
examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4
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@ -101,7 +101,7 @@ colvars: Creating proxy instance
colvars: ---------------------------------------------------------------------- colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16. colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013: colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594 colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation. colvars: in any publication based on this calculation.
colvars: SMP parallelism is available. colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29. colvars: Using LAMMPS interface, version 2018-08-29.
@ -405,7 +405,7 @@ colvars: Creating proxy instance
colvars: ---------------------------------------------------------------------- colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16. colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013: colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594 colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation. colvars: in any publication based on this calculation.
colvars: SMP parallelism is available. colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29. colvars: Using LAMMPS interface, version 2018-08-29.

2
examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1
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@ -100,7 +100,7 @@ colvars: Creating proxy instance
colvars: ---------------------------------------------------------------------- colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16. colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013: colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594 colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation. colvars: in any publication based on this calculation.
colvars: SMP parallelism is available. colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29. colvars: Using LAMMPS interface, version 2018-08-29.

2
examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4
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@ -100,7 +100,7 @@ colvars: Creating proxy instance
colvars: ---------------------------------------------------------------------- colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16. colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013: colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594 colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation. colvars: in any publication based on this calculation.
colvars: SMP parallelism is available. colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29. colvars: Using LAMMPS interface, version 2018-08-29.

6
examples/USER/misc/rhok/README.md
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@ -19,7 +19,7 @@ For future reference we note that the structure factor S(k) is given by the vari
It is recommended to get familiar with the interface pinning method by reading: It is recommended to get familiar with the interface pinning method by reading:
[Ulf R. Pedersen, JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747) [Ulf R. Pedersen, JCP 139, 104102 (2013)](https://doi.org/10.1063/1.4818747)
A detailed bibliography is provided at A detailed bibliography is provided at
@ -63,8 +63,8 @@ can be used to show this. The present directory contains the input files that we
the value fluctuates around the anchor point (a) -- showing that this is indeed a coexistence the value fluctuates around the anchor point (a) -- showing that this is indeed a coexistence
state point. state point.
The reference [JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747) gives details on using the method to find coexistence state points, The reference [JCP 139, 104102 (2013)](https://doi.org/10.1063/1.4818747) gives details on using the method to find coexistence state points,
and the reference [JCP 142, 044104 (2015)](http://dx.doi.org/10.1063/1.4818747) show how the crystal growth rate can be computed from fluctuations. and the reference [JCP 142, 044104 (2015)](https://doi.org/10.1063/1.4818747) show how the crystal growth rate can be computed from fluctuations.
That method have been experienced to be most effective in the slightly super-heated regime above the melting temperature. That method have been experienced to be most effective in the slightly super-heated regime above the melting temperature.
## Contact ## Contact

2
examples/USER/misc/ti/in.ti_spring
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@ -2,7 +2,7 @@
# #
# Description: nonequilibrium thermodynamic integration. Further details in: # Description: nonequilibrium thermodynamic integration. Further details in:
# R. Freitas, M. Asta, and M. de Koning, Computational Materials Science, (2016) # R. Freitas, M. Asta, and M. de Koning, Computational Materials Science, (2016)
# http://dx.doi.org/10.1016/j.commatsci.2015.10.050 # https://doi.org/10.1016/j.commatsci.2015.10.050
#--------------------------- System setup -------------------------------------# #--------------------------- System setup -------------------------------------#

2
lib/colvars/README
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@ -27,7 +27,7 @@ Also available is a Doxygen-based developer documentation:
The reference article is: The reference article is:
G. Fiorin, M. L. Klein, and J. Hénin, G. Fiorin, M. L. Klein, and J. Hénin,
Molecular Physics 111, 3345 (2013). Molecular Physics 111, 3345 (2013).
http://dx.doi.org/10.1080/00268976.2013.813594 https://doi.org/10.1080/00268976.2013.813594
## Requirements ## Requirements

2
lib/colvars/colvarmodule.cpp
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@ -50,7 +50,7 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
cvm::log("Initializing the collective variables module, version "+ cvm::log("Initializing the collective variables module, version "+
cvm::to_str(COLVARS_VERSION)+".\n"); cvm::to_str(COLVARS_VERSION)+".\n");
cvm::log("Please cite Fiorin et al, Mol Phys 2013:\n " cvm::log("Please cite Fiorin et al, Mol Phys 2013:\n "
"https://dx.doi.org/10.1080/00268976.2013.813594\n" "https://doi.org/10.1080/00268976.2013.813594\n"
"in any publication based on this calculation.\n"); "in any publication based on this calculation.\n");
if (proxy->smp_enabled() == COLVARS_OK) { if (proxy->smp_enabled() == COLVARS_OK) {

4
lib/linalg/iparam2stage.F
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@ -130,7 +130,7 @@
*> of 2011 International Conference for High Performance Computing, *> of 2011 International Conference for High Performance Computing,
*> Networking, Storage and Analysis (SC '11), New York, NY, USA, *> Networking, Storage and Analysis (SC '11), New York, NY, USA,
*> Article 8 , 11 pages. *> Article 8 , 11 pages.
*> http://doi.acm.org/10.1145/2063384.2063394 *> https://doi.acm.org/10.1145/2063384.2063394
*> *>
*> A. Haidar, J. Kurzak, P. Luszczek, 2013. *> A. Haidar, J. Kurzak, P. Luszczek, 2013.
*> An improved parallel singular value algorithm and its implementation *> An improved parallel singular value algorithm and its implementation
@ -138,7 +138,7 @@
*> for High Performance Computing, Networking, Storage and Analysis (SC '13). *> for High Performance Computing, Networking, Storage and Analysis (SC '13).
*> Denver, Colorado, USA, 2013. *> Denver, Colorado, USA, 2013.
*> Article 90, 12 pages. *> Article 90, 12 pages.
*> http://doi.acm.org/10.1145/2503210.2503292 *> https://doi.acm.org/10.1145/2503210.2503292
*> *>
*> A. Haidar, R. Solca, S. Tomov, T. Schulthess and J. Dongarra. *> A. Haidar, R. Solca, S. Tomov, T. Schulthess and J. Dongarra.
*> A novel hybrid CPU-GPU generalized eigensolver for electronic structure *> A novel hybrid CPU-GPU generalized eigensolver for electronic structure

2
potentials/AlSiMgCuFe.meam
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@ -1,7 +1,7 @@
# DATE: 2012-06-29 CONTRIBUTOR: Greg Wagner, gjwagne@sandia.gov CITATION: Jelinek, Groh, Horstemeyer, Houze, Kim, Wagner, Moitra and Baskes, Phys Rev B, 85, 245102 (2012) # DATE: 2012-06-29 CONTRIBUTOR: Greg Wagner, gjwagne@sandia.gov CITATION: Jelinek, Groh, Horstemeyer, Houze, Kim, Wagner, Moitra and Baskes, Phys Rev B, 85, 245102 (2012)
# MEAM Al, Si, Mg, Cu, Fe alloy potential # MEAM Al, Si, Mg, Cu, Fe alloy potential
# use with AlS SiS MgS CuS FeS from library.meam # use with AlS SiS MgS CuS FeS from library.meam
# http://dx.doi.org/10.1103/PhysRevB.85.245102 # https://doi.org/10.1103/PhysRevB.85.245102
Cmin(1,1,1) = 0.8 Cmin(1,1,1) = 0.8
repuls(1,1) = 0.1 repuls(1,1) = 0.1

4
potentials/CH.airebo-m
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@ -1,8 +1,8 @@
# DATE: 2016-03-15 CONTRIBUTOR: T.C. O'Connor CITATION: O'Connor, Andzelm, Robbins, J. Chem. Phys. 142, 024903 (2015) # DATE: 2016-03-15 CONTRIBUTOR: T.C. O'Connor CITATION: O'Connor, Andzelm, Robbins, J. Chem. Phys. 142, 024903 (2015)
# AIREBO-M of T.C. O'Connor, J.W. Andzelm, M.O. Robbins (2015) # AIREBO-M of T.C. O'Connor, J.W. Andzelm, M.O. Robbins (2015)
# Citation: J. Chem. Phys. 142, 024903 (2015); http://dx.doi.org/10.1063/1.4905549 # Citation: J. Chem. Phys. 142, 024903 (2015); https://doi.org/10.1063/1.4905549
# Based on AIREBO of S.J. Stuart, A.B. Tutein, J.A. Harrison (2000) # Based on AIREBO of S.J. Stuart, A.B. Tutein, J.A. Harrison (2000)
# Citation: J. Chem. Phys. 112, 6472 (2000); http://dx.doi.org/10.1063/1.481208 # Citation: J. Chem. Phys. 112, 6472 (2000); https://doi.org/10.1063/1.481208
1.7 rcmin_CC 1.7 rcmin_CC
1.3 rcmin_CH 1.3 rcmin_CH

5
python/lammps.py
View File

@ -486,6 +486,7 @@ class lammps(object):
return None return None
elif style == 2: elif style == 2:
self.lib.lammps_extract_compute.restype = POINTER(c_int) self.lib.lammps_extract_compute.restype = POINTER(c_int)
ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
return ptr[0] return ptr[0]
if type == 1: if type == 1:
self.lib.lammps_extract_compute.restype = POINTER(c_double) self.lib.lammps_extract_compute.restype = POINTER(c_double)
@ -509,6 +510,10 @@ class lammps(object):
result = ptr[0] result = ptr[0]
self.lib.lammps_free(ptr) self.lib.lammps_free(ptr)
return result return result
elif (style == 2) and (type == 0):
self.lib.lammps_extract_fix.restype = POINTER(c_int)
ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
return ptr[0]
elif (style == 1) or (style == 2): elif (style == 1) or (style == 2):
if type == 1: if type == 1:
self.lib.lammps_extract_fix.restype = POINTER(c_double) self.lib.lammps_extract_fix.restype = POINTER(c_double)

2
src/KOKKOS/pair_snap_kokkos.h
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@ -38,7 +38,7 @@ struct TagPairSNAPComputeNeigh{};
struct TagPairSNAPPreUi{}; struct TagPairSNAPPreUi{};
struct TagPairSNAPComputeUi{}; struct TagPairSNAPComputeUi{};
struct TagPairSNAPComputeUiTot{}; // accumulate ulist into ulisttot separately struct TagPairSNAPComputeUiTot{}; // accumulate ulist into ulisttot separately
struct TagPairSNAPComputeUiCPU{}; struct TagPairSNAPComputeUiCPU{};
struct TagPairSNAPComputeZi{}; struct TagPairSNAPComputeZi{};
struct TagPairSNAPComputeBi{}; struct TagPairSNAPComputeBi{};
struct TagPairSNAPZeroYi{}; struct TagPairSNAPZeroYi{};

6
src/KOKKOS/sna_kokkos.h
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@ -32,7 +32,7 @@ template <typename real>
struct alignas(2*sizeof(real)) SNAComplex struct alignas(2*sizeof(real)) SNAComplex
{ {
real re,im; real re,im;
KOKKOS_FORCEINLINE_FUNCTION SNAComplex() = default; KOKKOS_FORCEINLINE_FUNCTION SNAComplex() = default;
KOKKOS_FORCEINLINE_FUNCTION SNAComplex(real re) KOKKOS_FORCEINLINE_FUNCTION SNAComplex(real re)
@ -172,7 +172,7 @@ inline
static KOKKOS_FORCEINLINE_FUNCTION static KOKKOS_FORCEINLINE_FUNCTION
void caxpy(const SNAcomplex& a, const SNAcomplex& x, SNAcomplex& y); void caxpy(const SNAcomplex& a, const SNAcomplex& x, SNAcomplex& y);
// efficient complex FMA, conjugate of scalar // efficient complex FMA, conjugate of scalar
static KOKKOS_FORCEINLINE_FUNCTION static KOKKOS_FORCEINLINE_FUNCTION
void caconjxpy(const SNAcomplex& a, const SNAcomplex& x, SNAcomplex& y); void caconjxpy(const SNAcomplex& a, const SNAcomplex& x, SNAcomplex& y);
@ -201,7 +201,7 @@ inline
void grow_rij(int, int); void grow_rij(int, int);
int twojmax, diagonalstyle; int twojmax, diagonalstyle;
t_sna_2d_ll blist; t_sna_2d_ll blist;
t_sna_2c_ll ulisttot; t_sna_2c_ll ulisttot;
t_sna_2c_ll zlist; t_sna_2c_ll zlist;

2
src/MISC/fix_orient_bcc.cpp
View File

@ -15,7 +15,7 @@
Contributing authors: Koenraad Janssens and David Olmsted (SNL) Contributing authors: Koenraad Janssens and David Olmsted (SNL)
Modification for bcc provided by: Tegar Wicaksono (UBC) Modification for bcc provided by: Tegar Wicaksono (UBC)
For a tutorial, please see "Order parameters of crystals in LAMMPS" For a tutorial, please see "Order parameters of crystals in LAMMPS"
(https://dx.doi.org/10.6084/m9.figshare.1488628.v1 (https://doi.org/10.6084/m9.figshare.1488628.v1
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "fix_orient_bcc.h" #include "fix_orient_bcc.h"

2
src/USER-COLVARS/README
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@ -27,7 +27,7 @@ and in the reference article:
Using collective variables to drive molecular dynamics simulations, Using collective variables to drive molecular dynamics simulations,
G. Fiorin, M. L. Klein, and J. Henin, G. Fiorin, M. L. Klein, and J. Henin,
Molecular Physics 111, 3345 (2013) Molecular Physics 111, 3345 (2013)
http://dx.doi.org/10.1080/00268976.2013.813594 https://doi.org/10.1080/00268976.2013.813594
A reference manual for the package and library is included with the A reference manual for the package and library is included with the
LAMMPS doc pages: LAMMPS doc pages:

2
src/USER-MISC/compute_cnp_atom.cpp
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@ -12,7 +12,7 @@
Common Neighbor Parameter as proposed in: Common Neighbor Parameter as proposed in:
Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007) Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007)
Cite: http://dx.doi.org/10.1063/1.2197987 Cite: https://doi.org/10.1063/1.2197987
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

6
src/USER-MISC/compute_hma.cpp
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@ -31,16 +31,16 @@ More information about HMA is available in these publications:
A. J. Schultz, D. A. Kofke, “Comprehensive high-precision high-accuracy A. J. Schultz, D. A. Kofke, “Comprehensive high-precision high-accuracy
equation of state and coexistence properties for classical Lennard-Jones equation of state and coexistence properties for classical Lennard-Jones
crystals and low-temperature fluid phases”, J. Chem. Phys. 149, 204508 (2018) crystals and low-temperature fluid phases”, J. Chem. Phys. 149, 204508 (2018)
https://dx.doi.org/10.1063/1.5053714 https://doi.org/10.1063/1.5053714
S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Harmonically Assisted Methods for S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Harmonically Assisted Methods for
Computing the Free Energy of Classical Crystals by Molecular Simulation: A Computing the Free Energy of Classical Crystals by Molecular Simulation: A
Comparative Study”, J. Chem. Theory Comput. 13, 825-834 (2017) Comparative Study”, J. Chem. Theory Comput. 13, 825-834 (2017)
https://dx.doi.org/10.1021/acs.jctc.6b01082 https://doi.org/10.1021/acs.jctc.6b01082
S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Very fast averaging of thermal S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Very fast averaging of thermal
properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015) properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015)
https://dx.doi.org/10.1103/PhysRevE.92.043303 https://doi.org/10.1103/PhysRevE.92.043303
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath> #include <cmath>

2
src/USER-MISC/fix_filter_corotate.cpp
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@ -54,7 +54,7 @@ static const char cite_filter_corotate[] =
" Year = {2017},\n" " Year = {2017},\n"
" Pages = {180 - 198},\n" " Pages = {180 - 198},\n"
" Volume = {333},\n\n" " Volume = {333},\n\n"
" Doi = {http://dx.doi.org/10.1016/j.jcp.2016.12.024},\n" " Doi = {https://doi.org/10.1016/j.jcp.2016.12.024},\n"
" ISSN = {0021-9991},\n" " ISSN = {0021-9991},\n"
" Keywords = {Mollified impulse method},\n" " Keywords = {Mollified impulse method},\n"
" Url = {http://www.sciencedirect.com/science/article/pii/S0021999116306787}\n" " Url = {http://www.sciencedirect.com/science/article/pii/S0021999116306787}\n"

2
src/USER-MISC/fix_flow_gauss.cpp
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@ -37,7 +37,7 @@ static const char cite_flow_gauss[] =
"title = {The Dynamics of Water in Porous Two-Dimensional Crystals},\n" "title = {The Dynamics of Water in Porous Two-Dimensional Crystals},\n"
"volume = {121},\n" "volume = {121},\n"
"number = {1},\n" "number = {1},\n"
"url = {http://dx.doi.org/10.1021/acs.jpcb.6b09387},\n" "url = {https://doi.org/10.1021/acs.jpcb.6b09387},\n"
"doi = {10.1021/acs.jpcb.6b09387},\n" "doi = {10.1021/acs.jpcb.6b09387},\n"
"urldate = {2016-12-07},\n" "urldate = {2016-12-07},\n"
"journal = {J. Phys. Chem. B},\n" "journal = {J. Phys. Chem. B},\n"

4
src/USER-MISC/fix_grem.cpp
View File

@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Force scaling fix for gREM. Force scaling fix for gREM.
Cite: http://dx.doi.org/10.1063/1.3432176 Cite: https://doi.org/10.1063/1.3432176
Cite: http://dx.doi.org/10.1021/acs.jpcb.5b07614 Cite: https://doi.org/10.1021/acs.jpcb.5b07614
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

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

@ -37,7 +37,7 @@ static const char cite_momb[] =
" solution-phase synthesis of shape-selective Ag nanoparticles.},\n" " solution-phase synthesis of shape-selective Ag nanoparticles.},\n"
"volume = {118},\n" "volume = {118},\n"
"number = {6},\n" "number = {6},\n"
"url = {http://dx.doi.org/10.1021/jp412098n},\n" "url = {https://doi.org/10.1021/jp412098n},\n"
"doi = {10.1021/jp412098n},\n" "doi = {10.1021/jp412098n},\n"
"journal = {J. Phys. Chem. C},\n" "journal = {J. Phys. Chem. C},\n"
"author = {Zhou, Ya, Wissam A. Saidi, and Kristen A. Fichthorn},\n" "author = {Zhou, Ya, Wissam A. Saidi, and Kristen A. Fichthorn},\n"

4
src/USER-YAFF/README
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@ -1,8 +1,8 @@
This package implements the styles that are needed to use typical force fields This package implements the styles that are needed to use typical force fields
generated by QuickFF for the simulation of metal-organic frameworks. The generated by QuickFF for the simulation of metal-organic frameworks. The
QuickFF methodology is detailed in following papers: QuickFF methodology is detailed in following papers:
Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) http://dx.doi.org/10.1002/jcc.23877 Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) https://doi.org/10.1002/jcc.23877
Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) http://dx.doi.org/10.1002/jcc.25173 Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) https://doi.org/10.1002/jcc.25173
The corresponding software package can be found on http://molmod.github.io/QuickFF The corresponding software package can be found on http://molmod.github.io/QuickFF

35
src/library.cpp
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@ -537,35 +537,19 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
if (style == 1) { if (style == 1) {
if (!compute->peratom_flag) return NULL; if (!compute->peratom_flag) return NULL;
if (type == 1) { if (compute->invoked_peratom != lmp->update->ntimestep)
if (compute->invoked_peratom != lmp->update->ntimestep) compute->compute_peratom();
compute->compute_peratom(); if (type == 1) return (void *) compute->vector_atom;
return (void *) compute->vector_atom; if (type == 2) return (void *) compute->array_atom;
}
if (type == 2) {
if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->array_atom;
}
} }
if (style == 2) { if (style == 2) {
if (!compute->local_flag) return NULL; if (!compute->local_flag) return NULL;
if (type == 0) { if (compute->invoked_local != lmp->update->ntimestep)
if (compute->invoked_local != lmp->update->ntimestep) compute->compute_local();
compute->compute_local(); if (type == 0) return (void *) &compute->size_local_rows;
return (void *) &compute->size_local_rows; if (type == 1) return (void *) compute->vector_local;
} if (type == 2) return (void *) compute->array_local;
if (type == 1) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) compute->vector_local;
}
if (type == 2) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) compute->array_local;
}
} }
} }
END_CAPTURE END_CAPTURE
@ -637,6 +621,7 @@ void *lammps_extract_fix(void *ptr, char *id, int style, int type,
if (style == 2) { if (style == 2) {
if (!fix->local_flag) return NULL; if (!fix->local_flag) return NULL;
if (type == 0) return (void *) &fix->size_local_rows;
if (type == 1) return (void *) fix->vector_local; if (type == 1) return (void *) fix->vector_local;
if (type == 2) return (void *) fix->array_local; if (type == 2) return (void *) fix->array_local;
} }

2
src/min_cg.cpp
View File

@ -113,7 +113,7 @@ int MinCG::iterate(int maxiter)
if (update->ftol > 0.0) { if (update->ftol > 0.0) {
if (normstyle == MAX) fdotf = fnorm_max(); // max force norm if (normstyle == MAX) fdotf = fnorm_max(); // max force norm
else if (normstyle == INF) fdotf = fnorm_inf(); // infinite force norm else if (normstyle == INF) fdotf = fnorm_inf(); // infinite force norm
else if (normstyle == TWO) fdotf = fnorm_sqr(); // Euclidean force 2-norm else if (normstyle == TWO) fdotf = dotall[0]; // same as fnorm_sqr(), Euclidean force 2-norm
else error->all(FLERR,"Illegal min_modify command"); else error->all(FLERR,"Illegal min_modify command");
if (fdotf < update->ftol*update->ftol) return FTOL; if (fdotf < update->ftol*update->ftol) return FTOL;
} }