forked from lijiext/lammps
update of Fortran-DFTB interface to be compatible with fix msst
This commit is contained in:
Steve Plimpton
parent
3cd597e948
commit
59db5f6a17
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@ -25,7 +25,7 @@ keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} or {beta} or {dftb} :l
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{e0} value = initial total energy (energy units)
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{tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
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{dftb} value = {yes} or {no} for whether using MSST in conjunction with DFTB+
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{beta} value = scale factor on energy contribution of DFTB+ :pre
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{beta} value = scale factor for improved energy conservation :pre
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:ule
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[Examples:]
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@ -72,6 +72,14 @@ be calculated on the first step, after the energy specified by
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{tscale} is removed. The value of {e0} is not used in the dynamical
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equations, but is used in calculating the deviation from the Hugoniot.
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The keyword {beta} is a scaling term that can be added to the MSST
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ionic equations of motion to account for drift in the conserved
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quantity during long timescale simulations, similar to a Berendson
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thermostat. See "(Reed)"_#Reed and "(Goldman)"_#Goldman for more
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details. The value of {beta} must be between 0.0 and 1.0 inclusive.
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A value of 0.0 means no contribution, a value of 1.0 means a full
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contribution.
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Values of shockvel less than a critical value determined by the
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material response will not have compressive solutions. This will be
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reflected in lack of significant change of the volume in the MSST.
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@ -95,23 +103,15 @@ or "_MSST_pe". The group for the new computes is "all".
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:line
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The {dftb} and {beta} keywords are to allow this fix to be used when
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LAMMPS is being driven by DFTB+, a density-functional tight-binding
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code.
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If the keyword {dftb} is used with a value of {yes}, then the MSST
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equations are altered to account for an energy contribution compute by
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DFTB+. In this case, you must define a "fix
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external"_fix_external.html command in your input script, which is
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used to callback to DFTB+ during the LAMMPS timestepping. DFTB+ will
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communicate its info to LAMMPS via that fix.
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The keyword {beta} is a scale factor on the DFTB+ energy contribution.
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The value of {beta} must be between 0.0 and 1.0 inclusive. A value of
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0.0 means no contribution, a value of 1.0 means a full contribution.
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(July 2017) More information about these keywords and the use of
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LAMMPS with DFTB+ will be added to the LAMMMPS documention soon.
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The {dftb} keyword is to allow this fix to be used when LAMMPS is
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being driven by DFTB+, a density-functional tight-binding code. If the
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keyword {dftb} is used with a value of {yes}, then the MSST equations
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are altered to account for the electron entropy contribution to the
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Hugonio relations and total energy. See "(Reed2)"_#Reed2 and
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"(Goldman)"_#Goldman for details on this contribution. In this case,
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you must define a "fix external"_fix_external.html command in your
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input script, which is used to callback to DFTB+ during the LAMMPS
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timestepping. DFTB+ will communicate its info to LAMMPS via that fix.
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:line
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@ -182,4 +182,12 @@ timestep.
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:line
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:link(Reed)
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[(Reed)] Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003).
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[(Reed)] Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503
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(2003).
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:link(Reed2)
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[(Reed2)] Reed, J. Phys. Chem. C, 116, 2205 (2012).
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:link(Goldman)
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[(Goldman)] Goldman, Srinivasan, Hamel, Fried, Gaus, and Elstner,
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J. Phys. Chem. C, 117, 7885 (2013).
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@ -27,13 +27,34 @@ pair_coeff * * Ar Ar :pre
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[Description:]
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This pair style is a wrapper on the "Knowledge Base for Interatomic
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Models (KIM)"_https://openkim.org repository of interatomic potentials,
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so that they can be used by LAMMPS scripts.
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Models (OpenKIM)"_https://openkim.org repository of interatomic
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potentials, so that they can be used by LAMMPS scripts.
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In KIM lingo, a potential is a "model" and a model contains both the
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analytic formulas that define the potential as well as the parameters
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needed to run it for one or more materials, including coefficients and
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cutoffs.
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Note that in LAMMPS lingo, a KIM model driver is a pair style
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(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
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element or alloy and set of parameters, e.g. EAM for Cu with a
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specific EAM potential file.
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See the current list of "KIM model
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drivers"_https://openkim.org/kim-items/model-drivers/alphabetical.
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See the current list of all "KIM
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models"_https://openkim.org/kim-items/models/by-model-drivers
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See the list of "example KIM models"_https://openkim.org/kim-api which
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are included in the KIM library by default, in the "What is in the KIM
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API source package?" section.
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To use this pair style, you must first download and install the KIM
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API library from the "OpenKIM website"_https://openkim.org. The "KIM
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section of Section packages"_Section_packages.html#kim-package has
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instructions on how to do this with a simple make command, when
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building LAMMPS.
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See the examples/kim dir for an input script that uses a KIM model
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(potential) for Lennard-Jones.
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:line
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The argument {virialmode} determines how the global virial is
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calculated. If {KIMvirial} is specified, the KIM model performs the
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@ -41,8 +41,8 @@ fortran a simple wrapper on the LAMMPS library API that
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can be called from Fortran
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fortran2 a more sophisticated wrapper on the LAMMPS library API that
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can be called from Fortran
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fortran3 wrapper written by Nir Goldman (LLNL), as an
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fortran_dftb wrapper written by Nir Goldman (LLNL), as an
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extension to fortran2, used for calling LAMMPS
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from Fortran DFTB+ code
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from Fortran DFTB+ tight-binding code
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Each sub-directory has its own README with more details.
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@ -47,11 +47,35 @@ void lammps_set_callback (void *ptr) {
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return;
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}
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void lammps_set_external_vector_length (void *ptr, int n) {
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class LAMMPS *lmp = (class LAMMPS *) ptr;
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int ifix = lmp->modify->find_fix_by_style("external");
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FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
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fix->set_vector_length(n);
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return;
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}
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void lammps_set_external_vector (void *ptr, int n, double val) {
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class LAMMPS *lmp = (class LAMMPS *) ptr;
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int ifix = lmp->modify->find_fix_by_style("external");
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FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
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fix->set_vector (n, val);
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return;
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}
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void lammps_set_user_energy (void *ptr, double energy) {
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class LAMMPS *lmp = (class LAMMPS *) ptr;
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int ifix = lmp->modify->find_fix_by_style("external");
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FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
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fix->set_energy(energy);
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fix->set_energy_global(energy);
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return;
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}
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void lammps_set_user_virial (void *ptr, double *virial) {
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class LAMMPS *lmp = (class LAMMPS *) ptr;
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int ifix = lmp->modify->find_fix_by_style("external");
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FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
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fix->set_virial_global(virial);
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return;
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}
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@ -26,6 +26,9 @@ extern "C" {
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/* Prototypes for auxiliary functions */
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void lammps_set_callback (void *);
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void lammps_set_user_energy (void*, double);
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void lammps_set_user_virial (void*, double*);
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void lammps_set_external_vector_length (void*, int);
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void lammps_set_external_vector (void*, int, double);
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#ifdef __cplusplus
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}
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@ -52,12 +52,16 @@ module LAMMPS
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C_NULL_CHAR, C_loc, C_F_pointer, lammps_instance => C_ptr
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implicit none
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private
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public :: lammps_set_user_virial
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public :: lammps_set_external_vector_length
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public :: lammps_set_external_vector
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public :: lammps_set_user_energy
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public :: lammps_open, lammps_open_no_mpi, lammps_close, lammps_file, &
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lammps_command, lammps_free, lammps_extract_global, &
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lammps_extract_atom, lammps_extract_compute, lammps_extract_fix, &
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lammps_extract_variable, lammps_get_natoms, lammps_gather_atoms, &
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lammps_scatter_atoms, lammps_set_callback, lammps_set_user_energy
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public :: lammps_instance, C_ptr, C_double, C_int
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lammps_set_callback
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public :: lammps_scatter_atoms, lammps_instance, C_ptr, C_double, C_int
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!! Functions supplemental to the prototypes in library.h. {{{1
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!! The function definitions (in C++) are contained in LAMMPS-wrapper.cpp.
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@ -218,6 +222,28 @@ module LAMMPS
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real(C_double), value :: energy
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end subroutine lammps_set_user_energy
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subroutine lammps_set_user_virial (ptr, virial) &
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bind (C, name='lammps_set_user_virial')
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import :: C_ptr, C_double
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type (C_ptr), value :: ptr
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real(C_double) :: virial(6)
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end subroutine lammps_set_user_virial
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subroutine lammps_set_external_vector_length (ptr, n) &
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bind (C, name='lammps_set_external_vector_length')
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import :: C_ptr, C_double, C_int
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type(C_ptr), value :: ptr
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integer (C_int), value :: n
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end subroutine lammps_set_external_vector_length
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subroutine lammps_set_external_vector (ptr, n, val) &
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bind (C, name='lammps_set_external_vector')
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import :: C_ptr, C_int, C_double
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type (C_ptr), value :: ptr
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integer (C_int), value :: n
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real(C_double), value :: val
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end subroutine lammps_set_external_vector
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subroutine lammps_actual_gather_atoms (ptr, name, type, count, data) &
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bind (C, name='lammps_gather_atoms')
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import :: C_ptr, C_int, C_char
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@ -3,8 +3,9 @@ forces from a fortran code for a LAMMPS simulation. The reader should
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refer to the README file in COUPLE/fortran2 before proceeding. Here,
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the LAMMPS.F90 file has been modified slightly and additional files
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named LAMMPS-wrapper2.h and LAMMPS-wrapper2.cpp have been included in
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order to supply wrapper functions to set the LAMMPS callback function
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and total energy.
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order to supply wrapper functions to set the LAMMPS callback function,
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total energy, virial, and electronic entropy contribution (needed for
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MSST simulations with a quantum code).
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In this example, the callback function is set to run the
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semi-empirical quantum code DFTB+ in serial and then read in the total
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@ -20,11 +21,14 @@ etc.
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A few more important notes:
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-The stress tensor from DFTB+ is passed in to LAMMPS via pointer.
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-Calling the subroutine lammps_set_callback() is required in order to set
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a pointer to the callback function in LAMMPS.
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-The subroutine lammps_set_user_energy() passes in the potential energy
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from DFTB+ to LAMMPS.
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from DFTB+ to LAMMPS. Similarly, lammps_set_user_virial passes the stress tensor.
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-The electronic entropy contribution is set via lammps_set_external_vector(). Their needs
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to be a call to lammps_set_external_vector_length() before this value can be
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passed to LAMMPS.
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This example was created by Nir Goldman, whom you can contact with
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questions:
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@ -0,0 +1,40 @@
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#sample DFTB+ script to run this test code
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Geometry = GenFormat {
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<<< "lammps.gen"
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}
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Driver = {
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}
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Hamiltonian = DFTB {
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LAMMPS = Yes # keyword to print energy, forces, and stress tensor to file(results.out)
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SCC = No
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MaxAngularMomentum = {
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C = "p"
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}
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Charge = 0.0
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Eigensolver = Standard {}
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Filling = Fermi {
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Temperature [Kelvin] = 298.0
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}
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SlaterKosterFiles = Type2FileNames {
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Prefix = "~/slako/mio-1-1/" # the user must define the location of the skf files
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Separator = "-"
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Suffix = ".skf"
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LowerCaseTypeName = No
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}
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KPointsAndWeights = {
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0.0000000000000 0.0000000000000 0.0000000000000 1.00000000000000
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}
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}
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Options = {
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CalculateForces = Yes
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WriteDetailedOut = No
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WriteBandOut = No
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RandomSeed = 12345
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}
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ParserOptions = {
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ParserVersion = 3
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}
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@ -0,0 +1,129 @@
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Geometry = GenFormat {
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64 S
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C
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1 1 7.099007 7.117657 7.119139
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2 1 0.858709 0.867233 0.882294
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3 1 1.772527 1.811776 7.120239
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4 1 2.702145 2.681271 0.901362
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5 1 0.017539 1.794455 1.788454
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6 1 0.885593 2.694118 2.707994
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7 1 1.795055 7.120787 1.777896
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8 1 2.642849 0.868278 2.670699
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9 1 0.016060 0.017156 3.568644
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10 1 0.891891 0.896406 4.439286
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11 1 1.766086 1.764402 3.550134
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12 1 2.677349 2.648926 4.427174
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13 1 0.010133 1.771283 5.342173
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14 1 0.858153 2.653565 6.241596
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15 1 1.804087 0.020636 5.353268
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16 1 2.689680 0.907188 6.224575
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17 1 0.017845 3.577563 7.113016
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18 1 0.910027 4.459286 0.910286
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19 1 1.766394 5.376046 0.015526
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20 1 2.683727 6.220728 0.898553
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21 1 0.003357 5.363423 1.774139
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22 1 0.856735 6.238324 2.660213
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23 1 1.761079 3.549776 1.797054
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24 1 2.667227 4.463441 2.646074
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25 1 7.132499 3.551558 3.599764
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26 1 0.920387 4.482191 4.479257
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27 1 1.772194 5.337132 3.555569
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28 1 2.675010 6.251629 4.483124
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29 1 0.005702 5.371095 5.351147
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30 1 0.880807 6.249819 6.264231
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31 1 1.793177 3.592396 5.369939
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32 1 2.653179 4.463595 6.274044
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33 1 3.557243 7.118913 0.026006
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34 1 4.458971 0.889331 0.904950
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35 1 5.367903 1.759757 7.104941
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36 1 6.271565 2.658454 0.890168
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37 1 3.591915 1.768681 1.793880
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38 1 4.435612 2.662184 2.676722
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39 1 5.371040 0.000196 1.783464
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40 1 6.226453 0.886640 2.653384
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41 1 3.583339 0.005449 3.600177
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42 1 4.453692 0.909417 4.459713
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43 1 5.314554 1.805409 3.584215
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44 1 6.210181 2.642660 4.486206
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45 1 3.545704 1.802745 5.365369
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46 1 4.476660 2.701226 6.220451
|
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47 1 5.332820 0.029557 5.347965
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48 1 6.215725 0.915081 6.230289
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49 1 3.536446 3.551469 7.106600
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50 1 4.451181 4.426439 0.900180
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51 1 5.368735 5.377996 7.109524
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52 1 6.230666 6.220985 0.862175
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53 1 3.596626 5.372822 1.797613
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||||
54 1 4.485613 6.221252 2.699652
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||||
55 1 5.364421 3.549838 1.796281
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||||
56 1 6.261739 4.459046 2.648152
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||||
57 1 3.588752 3.581054 3.581755
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||||
58 1 4.462342 4.467270 4.478800
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59 1 5.355202 5.318323 3.556531
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60 1 6.268570 6.259831 4.465795
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61 1 3.588636 5.354278 5.362327
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62 1 4.475747 6.263866 6.227803
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63 1 5.331158 3.554349 5.318368
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64 1 6.254581 4.436344 6.209681
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0.0 0.0 0.0
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7.13400000000000 0 0
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0 7.13400000000000 0
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0 0 7.13400000000000
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}
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Driver = {}
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Hamiltonian = DFTB {
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LAMMPS = Yes
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SCC = No
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MaxAngularMomentum = {
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C = "p"
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}
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Charge = 0.0
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Eigensolver = Standard {}
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Filling = Fermi {
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Temperature [Kelvin] = 298.0
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IndependentKFilling = No
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}
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SlaterKosterFiles = Type2FileNames {
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Prefix = "~/slako/mio-1-1/"
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Separator = "-"
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Suffix = ".skf"
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LowerCaseTypeName = No
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}
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KPointsAndWeights = {
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0.0000000000000 0.0000000000000 0.0000000000000 1.00000000000000
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}
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PolynomialRepulsive = {}
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OldRepulsiveSum = No
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OrbitalResolvedSCC = No
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OldSKInterpolation = No
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NoErep = No
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Dispersion = {}
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ThirdOrder = No
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ThirdOrderFull = No
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}
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Options = {
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CalculateForces = Yes
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WriteDetailedOut = No
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WriteBandOut = No
|
||||
RandomSeed = 12345
|
||||
MullikenAnalysis = No
|
||||
WriteEigenvectors = No
|
||||
WriteAutotestTag = No
|
||||
WriteDetailedXML = No
|
||||
WriteResultsTag = No
|
||||
AtomResolvedEnergies = No
|
||||
WriteHS = No
|
||||
WriteRealHS = No
|
||||
MinimiseMemoryUsage = No
|
||||
ShowFoldedCoords = No
|
||||
}
|
||||
ParserOptions = {
|
||||
ParserVersion = 3
|
||||
WriteHSDInput = Yes
|
||||
WriteXMLInput = No
|
||||
StopAfterParsing = No
|
||||
IgnoreUnprocessedNodes = No
|
||||
}
|
||||
Analysis = {
|
||||
ProjectStates = {}
|
||||
}
|
||||
|
|
@ -0,0 +1,71 @@
|
|||
LAMMPS (6 Jul 2017)
|
||||
units real
|
||||
atom_style charge
|
||||
atom_modify map array
|
||||
atom_modify sort 0 0.0
|
||||
read_data data.diamond
|
||||
triclinic box = (0 0 0) to (7.134 7.134 7.134) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
64 atoms
|
||||
reading velocities ...
|
||||
64 velocities
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
fix 1 all nve
|
||||
fix 2 all external pf/callback 1 1
|
||||
|
||||
fix_modify 2 energy yes
|
||||
thermo_style custom step temp etotal ke pe lx ly lz pxx pyy pzz press
|
||||
|
||||
thermo 1
|
||||
timestep 0.5
|
||||
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 7.134, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.3 | 2.3 | 2.3 Mbytes
|
||||
Step Temp TotEng KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Press
|
||||
0 298.24835 -69593.587 56.008365 -69649.595 7.134 7.134 7.134 -19980.19 -21024.038 -21097.458 -20700.562
|
||||
1 295.24358 -69593.585 55.444098 -69649.029 7.134 7.134 7.134 -19778.833 -20799.657 -20854.156 -20477.549
|
||||
2 286.37211 -69593.58 53.778115 -69647.358 7.134 7.134 7.134 -19227.52 -20177.28 -20176.12 -19860.306
|
||||
3 272.062 -69593.572 51.090804 -69644.663 7.134 7.134 7.134 -18360.869 -19189.684 -19100.021 -18883.525
|
||||
4 253.01834 -69593.561 47.514575 -69641.075 7.134 7.134 7.134 -17198.143 -17855.03 -17652.036 -17568.403
|
||||
5 230.19242 -69593.547 43.228073 -69636.775 7.134 7.134 7.134 -15750.247 -16183.764 -15854.145 -15929.386
|
||||
6 204.71787 -69593.533 38.44418 -69631.977 7.134 7.134 7.134 -14083.498 -14247.434 -13789.835 -14040.256
|
||||
7 177.82397 -69593.518 33.393748 -69626.911 7.134 7.134 7.134 -12340.963 -12202.878 -11623.171 -12055.671
|
||||
8 150.76736 -69593.503 28.312758 -69621.816 7.134 7.134 7.134 -10637.824 -10180.827 -9495.0496 -10104.567
|
||||
9 124.7737 -69593.49 23.431383 -69616.921 7.134 7.134 7.134 -9113.3842 -8339.0492 -7572.8076 -8341.747
|
||||
10 100.98183 -69593.478 18.963481 -69612.442 7.134 7.134 7.134 -7833.9349 -6756.9749 -5945.8968 -6845.6022
|
||||
Loop time of 2.20497 on 1 procs for 10 steps with 64 atoms
|
||||
|
||||
Performance: 0.196 ns/day, 122.499 hours/ns, 4.535 timesteps/s
|
||||
0.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 1.4305e-06 | 1.4305e-06 | 1.4305e-06 | 0.0 | 0.00
|
||||
Comm | 4.22e-05 | 4.22e-05 | 4.22e-05 | 0.0 | 0.00
|
||||
Output | 0.00067687 | 0.00067687 | 0.00067687 | 0.0 | 0.03
|
||||
Modify | 2.2042 | 2.2042 | 2.2042 | 0.0 | 99.96
|
||||
Other | | 6.533e-05 | | | 0.00
|
||||
|
||||
Nlocal: 64 ave 64 max 64 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -21,7 +21,7 @@ liblammps_fortran.so : LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
|
|||
$(FC) $(FFLAGS) -shared -o $@ $^
|
||||
|
||||
simpleF.x: simple.o LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
|
||||
$(FC) $(FFLAGS) simple.o -o simpleF.x liblammps_fortran.a $(LAMMPS_SRC)/liblammps_mvapich.a -lstdc++ /usr/local/tools/fftw/lib/libfftw.a
|
||||
$(FC) $(FFLAGS) simple.o -o simpleF.x liblammps_fortran.a $(LAMMPS_SRC)/liblammps_mvapich.a -lstdc++ /usr/lib64/libfftw3.a
|
||||
|
||||
liblammps_fortran.a : LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
|
||||
$(AR) rs $@ $^
|
||||
|
|
@ -13,7 +13,7 @@
|
|||
type(c_ptr) :: c_pos, c_fext, c_ids
|
||||
double precision, pointer :: fext(:,:), pos(:,:)
|
||||
integer, intent(in) :: ids(nlocal)
|
||||
real (C_double), dimension(:), pointer :: virial => NULL()
|
||||
real(C_double) :: virial(6)
|
||||
real (C_double) :: etot
|
||||
real(C_double), pointer :: ts_lmp
|
||||
double precision :: stress(3,3), ts_dftb
|
||||
|
|
@ -61,26 +61,21 @@
|
|||
read(10,*)stress(i,:)
|
||||
enddo
|
||||
stress (:,:) = stress(:,:)*autoatm
|
||||
etot = etot*econv
|
||||
call lammps_extract_global(ts_lmp, lmp, 'TS_dftb')
|
||||
ts_lmp = ts_dftb
|
||||
do i = 1, nlocal
|
||||
read(10,*)fext(:,ids(i))
|
||||
fext(:,ids(i)) = fext(:,ids(i))*fconv
|
||||
enddo
|
||||
close(10)
|
||||
call lammps_set_user_energy (lmp, etot)
|
||||
call lammps_extract_atom (virial, lmp, 'virial')
|
||||
if (.not. associated(virial)) then
|
||||
print*,'virial pointer not associated.'
|
||||
STOP
|
||||
endif
|
||||
virial(1) = stress(1,1)/(nktv2p/volume)
|
||||
virial(2) = stress(2,2)/(nktv2p/volume)
|
||||
virial(3) = stress(3,3)/(nktv2p/volume)
|
||||
virial(4) = stress(1,2)/(nktv2p/volume)
|
||||
virial(5) = stress(1,3)/(nktv2p/volume)
|
||||
virial(6) = stress(2,3)/(nktv2p/volume)
|
||||
etot = etot*econv
|
||||
call lammps_set_external_vector(lmp,1,ts_dftb*econv)
|
||||
do i = 1, nlocal
|
||||
read(10,*)fext(:,ids(i))
|
||||
fext(:,ids(i)) = fext(:,ids(i))*fconv
|
||||
enddo
|
||||
close(10)
|
||||
call lammps_set_user_energy (lmp, etot)
|
||||
call lammps_set_user_virial (lmp, virial)
|
||||
|
||||
end subroutine
|
||||
end module callback
|
||||
|
|
@ -103,6 +98,7 @@ program simple_fortran_callback
|
|||
call lammps_open_no_mpi ('lmp -log log.simple', lmp)
|
||||
call lammps_file (lmp, 'in.simple')
|
||||
call lammps_set_callback(lmp)
|
||||
call lammps_set_external_vector_length(lmp,2)
|
||||
|
||||
call lammps_command (lmp, 'run 10')
|
||||
call lammps_close (lmp)
|
||||
|
|
@ -1,34 +1,27 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# Install.py tool to do automate build of Colvars
|
||||
# install.py tool to do a generic build of a library
|
||||
# soft linked to by many of the lib/Install.py files
|
||||
# used to automate the steps described in the corresponding lib/README
|
||||
|
||||
from __future__ import print_function
|
||||
import sys,os,subprocess
|
||||
import sys,commands,os
|
||||
|
||||
# help message
|
||||
|
||||
help = """
|
||||
Syntax from src dir: make lib-colvars args="-m machine -e suffix"
|
||||
Syntax from lib/colvars dir: python Install.py -m machine -e suffix
|
||||
|
||||
specify -m and optionally -e, order does not matter
|
||||
|
||||
Syntax: python Install.py -m machine -e suffix
|
||||
specify -m and optionally -e, order does not matter
|
||||
-m = peform a clean followed by "make -f Makefile.machine"
|
||||
machine = suffix of a lib/colvars/Makefile.* or of a
|
||||
src/MAKE/MACHINES/Makefile.* file
|
||||
machine = suffix of a lib/Makefile.* file
|
||||
-e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
|
||||
does not alter existing Makefile.machine
|
||||
|
||||
Examples:
|
||||
|
||||
make lib-colvars args="-m g++" # build COLVARS lib with GNU g++ compiler
|
||||
"""
|
||||
|
||||
# print error message or help
|
||||
|
||||
def error(str=None):
|
||||
if not str: print(help)
|
||||
else: print("ERROR"),str
|
||||
if not str: print help
|
||||
else: print "ERROR",str
|
||||
sys.exit()
|
||||
|
||||
# parse args
|
||||
|
|
@ -38,17 +31,17 @@ nargs = len(args)
|
|||
if nargs == 0: error()
|
||||
|
||||
machine = None
|
||||
extraflag = False
|
||||
extraflag = 0
|
||||
|
||||
iarg = 0
|
||||
while iarg < nargs:
|
||||
if args[iarg] == "-m":
|
||||
if iarg+2 > len(args): error()
|
||||
if iarg+2 > nargs: error()
|
||||
machine = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-e":
|
||||
if iarg+2 > len(args): error()
|
||||
extraflag = True
|
||||
if iarg+2 > nargs: error()
|
||||
extraflag = 1
|
||||
suffix = args[iarg+1]
|
||||
iarg += 2
|
||||
else: error()
|
||||
|
|
@ -58,85 +51,32 @@ while iarg < nargs:
|
|||
cwd = os.getcwd()
|
||||
lib = os.path.basename(cwd)
|
||||
|
||||
def get_lammps_machine_flags(machine):
|
||||
"""Parse Makefile.machine from LAMMPS, return dictionary of compiler flags"""
|
||||
if not os.path.exists("../../src/MAKE/MACHINES/Makefile.%s" % machine):
|
||||
error("Cannot locate src/MAKE/MACHINES/Makefile.%s" % machine)
|
||||
lines = open("../../src/MAKE/MACHINES/Makefile.%s" % machine,
|
||||
'r').readlines()
|
||||
machine_flags = {}
|
||||
for line in lines:
|
||||
line = line.partition('#')[0]
|
||||
line = line.rstrip()
|
||||
words = line.split()
|
||||
if (len(words) > 2):
|
||||
if ((words[0] == 'CC') or (words[0] == 'CCFLAGS') or
|
||||
(words[0] == 'SHFLAGS') or (words[0] == 'ARCHIVE') or
|
||||
(words[0] == 'ARFLAGS') or (words[0] == 'SHELL')):
|
||||
machine_flags[words[0]] = ' '.join(words[2:])
|
||||
return machine_flags
|
||||
|
||||
def gen_colvars_makefile_machine(machine, machine_flags):
|
||||
"""Generate Makefile.machine for Colvars given the compiler flags"""
|
||||
machine_makefile = open("Makefile.%s" % machine, 'w')
|
||||
machine_makefile.write('''# -*- makefile -*- to build Colvars module with %s
|
||||
|
||||
COLVARS_LIB = libcolvars.a
|
||||
COLVARS_OBJ_DIR =
|
||||
|
||||
CXX = %s
|
||||
CXXFLAGS = %s %s
|
||||
AR = %s
|
||||
ARFLAGS = %s
|
||||
SHELL = %s
|
||||
|
||||
include Makefile.common
|
||||
|
||||
.PHONY: default clean
|
||||
|
||||
default: $(COLVARS_LIB) Makefile.lammps
|
||||
|
||||
clean:
|
||||
-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
|
||||
''' % (machine, machine_flags['CC'],
|
||||
machine_flags['CCFLAGS'], machine_flags['SHFLAGS'] ,
|
||||
machine_flags['ARCHIVE'], machine_flags['ARFLAGS'],
|
||||
machine_flags['SHELL']))
|
||||
|
||||
if not os.path.exists("Makefile.%s" % machine):
|
||||
machine_flags = get_lammps_machine_flags(machine)
|
||||
gen_colvars_makefile_machine(machine, machine_flags)
|
||||
# create Makefile.auto as copy of Makefile.machine
|
||||
# reset EXTRAMAKE if requested
|
||||
|
||||
if not os.path.exists("Makefile.%s" % machine):
|
||||
error("lib/%s/Makefile.%s does not exist" % (lib,machine))
|
||||
|
||||
# create Makefile.auto as copy of Makefile.machine
|
||||
# reset EXTRAMAKE if requested
|
||||
|
||||
lines = open("Makefile.%s" % machine,'r').readlines()
|
||||
fp = open("Makefile.auto",'w')
|
||||
|
||||
for line in lines:
|
||||
words = line.split()
|
||||
if len(words) == 3 and extraflag and \
|
||||
words[0] == "EXTRAMAKE" and words[1] == '=':
|
||||
line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
|
||||
fp.write(line)
|
||||
print >>fp,line,
|
||||
|
||||
fp.close()
|
||||
|
||||
# make the library via Makefile.auto
|
||||
|
||||
try:
|
||||
import multiprocessing
|
||||
n_cpus = multiprocessing.cpu_count()
|
||||
except:
|
||||
n_cpus = 1
|
||||
print "Building lib%s.a ..." % lib
|
||||
cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
|
||||
txt = commands.getoutput(cmd)
|
||||
print txt
|
||||
|
||||
print("Building lib%s.a ..." % lib)
|
||||
cmd = ["make -f Makefile.auto clean"]
|
||||
print(subprocess.check_output(cmd, shell=True).decode())
|
||||
cmd = ["make -f Makefile.auto -j%d" % n_cpus]
|
||||
print(subprocess.check_output(cmd, shell=True).decode())
|
||||
|
||||
if os.path.exists("lib%s.a" % lib): print("Build was successful")
|
||||
if os.path.exists("lib%s.a" % lib): print "Build was successful"
|
||||
else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
|
||||
if not os.path.exists("Makefile.lammps"):
|
||||
print("lib/%s/Makefile.lammps was NOT created" % lib)
|
||||
print "lib/%s/Makefile.lammps was NOT created" % lib
|
||||
|
|
|
|||
Loading…
Reference in New Issue