diff --git a/.gitignore b/.gitignore index f9dda49da6..52b8212b13 100644 --- a/.gitignore +++ b/.gitignore @@ -26,6 +26,7 @@ vgcore.* .vagrant \#*# .#* +.vscode .DS_Store .DS_Store? diff --git a/doc/src/min_modify.rst b/doc/src/min_modify.rst index 0e586e8fe0..48981dbbba 100644 --- a/doc/src/min_modify.rst +++ b/doc/src/min_modify.rst @@ -15,7 +15,7 @@ Syntax .. parsed-literal:: - keyword = *dmax* or *line* or *norm* or *alpha_damp* or *discrete_factor* + keyword = *dmax* or *line* or *norm* or *alpha_damp* or *discrete_factor* or *integrator* or *tmax* *dmax* value = max max = maximum distance for line search to move (distance units) *line* value = *backtrack* or *quadratic* or *forcezero* or *spin_cubic* or *spin_none* @@ -28,6 +28,10 @@ Syntax damping = fictitious Gilbert damping for spin minimization (adim) *discrete_factor* value = factor factor = discretization factor for adaptive spin timestep (adim) + *integrator* value = *eulerimplicit* or *verlet* + time integration scheme for fire minimization + *tmax* value = factor + factor = maximum adaptive timestep for fire minimization (adim) @@ -38,6 +42,7 @@ Examples .. parsed-literal:: min_modify dmax 0.2 + min_modify integrator verlet tmax 4 Description """"""""""" @@ -60,32 +65,30 @@ highly overlapped atoms from being moved long distances (e.g. through another atom) due to large forces. The choice of line search algorithm for the *cg* and *sd* minimization -styles can be selected via the *line* keyword. -The default *quadratic* line search algorithm starts out using -the robust backtracking method described below. However, once -the system gets close to a local -minimum and the linesearch steps get small, so that the energy -is approximately quadratic in the step length, it uses the -estimated location of zero gradient as the linesearch step, -provided the energy change is downhill. -This becomes more efficient than backtracking -for highly-converged relaxations. The *forcezero* -line search algorithm is similar to *quadratic*\ . -It may be more efficient than *quadratic* on some systems. +styles can be selected via the *line* keyword. The default +*quadratic* line search algorithm starts out using the robust +backtracking method described below. However, once the system gets +close to a local minimum and the linesearch steps get small, so that +the energy is approximately quadratic in the step length, it uses the +estimated location of zero gradient as the linesearch step, provided +the energy change is downhill. This becomes more efficient than +backtracking for highly-converged relaxations. The *forcezero* line +search algorithm is similar to *quadratic*\ . It may be more +efficient than *quadratic* on some systems. -The backtracking search is robust and should always find a local energy -minimum. However, it will "converge" when it can no longer reduce the -energy of the system. Individual atom forces may still be larger than -desired at this point, because the energy change is measured as the -difference of two large values (energy before and energy after) and -that difference may be smaller than machine epsilon even if atoms -could move in the gradient direction to reduce forces further. +The backtracking search is robust and should always find a local +energy minimum. However, it will "converge" when it can no longer +reduce the energy of the system. Individual atom forces may still be +larger than desired at this point, because the energy change is +measured as the difference of two large values (energy before and +energy after) and that difference may be smaller than machine epsilon +even if atoms could move in the gradient direction to reduce forces +further. -The choice of a norm can be modified for the min styles *cg*\ , *sd*\ , -*quickmin*\ , *fire*\ , *spin*\ , *spin/cg* and *spin/lbfgs* using -the *norm* keyword. -The default *two* norm computes the 2-norm (Euclidean length) of the -global force vector: +The choice of a norm can be modified for the min styles *cg*\ , *sd*\ +, *quickmin*\ , *fire*\ , *fire/old*\ , *spin*\ , *spin/cg* and +*spin/lbfgs* using the *norm* keyword. The default *two* norm computes +the 2-norm (Euclidean length) of the global force vector: .. image:: Eqs/norm_two.jpg :align: center @@ -106,31 +109,64 @@ all atoms in the system: For the min styles *spin*\ , *spin/cg* and *spin/lbfgs*\ , the force norm is replaced by the spin-torque norm. -Keywords *alpha\_damp* and *discrete\_factor* only make sense when a -:doc:`min_spin ` command is declared. Keyword *alpha\_damp* -defines an analog of a magnetic Gilbert damping. It defines a relaxation -rate toward an equilibrium for a given magnetic system. Keyword -*discrete\_factor* defines a discretization factor for the adaptive -timestep used in the *spin* minimization. See :doc:`min_spin -` for more information about those quantities. +Keywords *alpha\_damp* and *discrete\_factor* only make sense when +a :doc:`min_spin ` command is declared. +Keyword *alpha\_damp* defines an analog of a magnetic Gilbert +damping. It defines a relaxation rate toward an equilibrium for +a given magnetic system. +Keyword *discrete\_factor* defines a discretization factor for the +adaptive timestep used in the *spin* minimization. +See :doc:`min_spin ` for more information about those +quantities. -The choice of a line search algorithm for the *spin/cg* and *spin/lbfgs* -styles can be specified via the *line* keyword. The *spin\_cubic* and -*spin\_none* options only make sense when one of those two minimization -styles is declared. The *spin\_cubic* option performs the line search -based on a cubic interpolation of the energy along the search -direction. The *spin\_none* option deactivates the line search -procedure. The *spin\_none* option is a default value for *line* -keyword for both *spin/lbfgs* and *spin/cg*\ . Convergence of -*spin/lbfgs* can be more robust if *spin\_cubic* line search is used. +The choice of a line search algorithm for the *spin/cg* and +*spin/lbfgs* styles can be specified via the *line* keyword. The +*spin\_cubic* and *spin\_none* keywords only make sense when one of those two +minimization styles is declared. The *spin\_cubic* performs the line +search based on a cubic interpolation of the energy along the search +direction. The *spin\_none* keyword deactivates the line search +procedure. The *spin\_none* is a default value for *line* keyword for +both *spin/lbfgs* and *spin/cg*\ . Convergence of *spin/lbfgs* can be +more robust if *spin\_cubic* line search is used. + +The Newton *integrator* used for *fire* minimization can be selected +to be either the symplectic Euler (\ *eulerimplicit*\ ) or velocity +Verlet (\ *verlet*\ ). *tmax* defines the maximum value for the +adaptive timestep during a *fire* minimization. It is a multiplication +factor applied to the current :doc:`timestep ` (not in time +unit). For example, *tmax* = 4.0 with a :doc:`timestep ` of +2fs, means that the maximum value the timestep can reach during a *fire* +minimization is 4fs. +Note that parameter defaults has been chosen to be reliable in most cases, +but one should consider adjusting :doc:`timestep ` and *tmax* to +optimize the minimization for large or complex systems. Other +parameters of the *fire* minimization can be tuned (\ *tmin*\ , +*delaystep*\ , *dtgrow*\ , *dtshrink*\ , *alpha0*\ , and +*alphashrink*\ ). Please refer to the references describing the +:doc:`min_style ` *fire*. +An additional stopping criteria *vdfmax* is used by *fire* in order to avoid +unnecessary looping when it is reasonable to think the system will not +be relaxed further. Note that in this case the system will NOT have +reached your minimization criteria. This could happen when the system +comes to be stuck in a local basin of the phase space. *vdfmax* is +the maximum number of consecutive iterations with P(t) < 0. + +The :doc:`min_style ` *fire* is an optimized implementation of +:doc:`min_style ` *fire/old*. It can however behave similarly +to the *fire/old* style by using the following set of parameters: + +.. parsed-literal:: + min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 & + dtgrow 1.1 dtshrink 0.5 alpha0 0.1 alphashrink 0.99 & + vdfmax 100000 halfstepback no initialdelay no Restrictions """""""""""" -For magnetic GNEB calculations, only the *spin\_none* value for *line* keyword can be used -when minimization styles *spin/cg* and *spin/lbfgs* are employed. -See :doc:`neb/spin ` for more explanations. +For magnetic GNEB calculations, only *spin\_none* value for *line* +keyword can be used when minimization styles *spin/cg* and *spin/lbfgs* are +employed. See :doc:`neb/spin ` for more explanation. Related commands """""""""""""""" @@ -142,6 +178,11 @@ Default The option defaults are dmax = 0.1, line = quadratic and norm = two. -For the *spin*\ , *spin/cg* and *spin/lbfgs* styles, the -option defaults are alpha\_damp = 1.0, discrete\_factor = 10.0, -line = spin\_none, and norm = euclidean. +For the *spin*\ , *spin/cg* and *spin/lbfgs* styles, the option +defaults are alpha\_damp = 1.0, discrete\_factor = 10.0, line = +spin\_none, and norm = euclidean. + +For the *fire* style, the option defaults are integrator = +eulerimplicit, tmax = 10.0, tmin = 0.02, delaystep = 20, dtgrow = 1.1, +dtshrink = 0.5, alpha0 = 0.25, alphashrink = 0.99, vdfmax = 2000, +halfstepback = yes and initialdelay = yes. diff --git a/doc/src/min_style.rst b/doc/src/min_style.rst index 48dad03567..5de407b6a9 100644 --- a/doc/src/min_style.rst +++ b/doc/src/min_style.rst @@ -11,7 +11,7 @@ Syntax min_style style -* style = *cg* or *hftn* or *sd* or *quickmin* or *fire* or *spin* or *spin/cg* or *spin/lbfgs* +* style = *cg* or *hftn* or *sd* or *quickmin* or *fire* or *fire/old* or *spin* or *spin/cg* or *spin/lbfgs* Examples """""""" @@ -26,8 +26,8 @@ Examples Description """"""""""" -Choose a minimization algorithm to use when a :doc:`minimize ` -command is performed. +Choose a minimization algorithm to use when a :doc:`minimize +` command is performed. Style *cg* is the Polak-Ribiere version of the conjugate gradient (CG) algorithm. At each iteration the force gradient is combined with the @@ -55,52 +55,68 @@ descent will not converge as quickly as CG, but may be more robust in some situations. Style *quickmin* is a damped dynamics method described in -:ref:`(Sheppard) `, where the damping parameter is related to the -projection of the velocity vector along the current force vector for -each atom. The velocity of each atom is initialized to 0.0 by this -style, at the beginning of a minimization. +:ref:`(Sheppard) `, where the damping parameter is related +to the projection of the velocity vector along the current force +vector for each atom. The velocity of each atom is initialized to 0.0 +by this style, at the beginning of a minimization. -Style *fire* is a damped dynamics method described in -:ref:`(Bitzek) `, which is similar to *quickmin* but adds a variable -timestep and alters the projection operation to maintain components of -the velocity non-parallel to the current force vector. The velocity -of each atom is initialized to 0.0 by this style, at the beginning of -a minimization. +Style *fire* is a damped dynamics method described in :ref:`(Bitzek) +`, which is similar to *quickmin* but adds a variable timestep +and alters the projection operation to maintain components of the +velocity non-parallel to the current force vector. The velocity of +each atom is initialized to 0.0 by this style, at the beginning of a +minimization. This style correspond to an optimized version described +in :ref:`(Guenole) ` that include different time integration +schemes and defaults parameters. The default parameters can be +modified with the command :doc:`min_modify `. -Style *spin* is a damped spin dynamics with an adaptive -timestep. -Style *spin/cg* uses an orthogonal spin optimization (OSO) -combined to a conjugate gradient (CG) approach to minimize spin -configurations. +Style *fire/old* is the original implementation of *fire* in Lammps, +conserved for backward compatibility. The main differences regarding +the current version *fire* are: time integration by Explicit Euler +only, different sequence in maintaining velocity components non-parallel +to the current force vector and hard-coded minimization parameters. +A complete description of the differences between *fire/old* and *fire* +can be found in :ref:`(Guenole) ` (where the current *fire* +in lammps is named *fire2.0*). By using an appropriate set of +parameters, *fire* can behave similarly than *fire/old*, as described +in the :doc:`min_modify ` command. -Style *spin/lbfgs* uses an orthogonal spin optimization (OSO) -combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno -(LBFGS) approach to minimize spin configurations. +Style *spin* is a damped spin dynamics with an adaptive timestep. -See the :doc:`min/spin ` doc page for more information -about the *spin*\ , *spin/cg* and *spin/lbfgs* styles. +Style *spin/cg* uses an orthogonal spin optimization (OSO) combined to +a conjugate gradient (CG) approach to minimize spin configurations. -Either the *quickmin* and *fire* styles are useful in the context of -nudged elastic band (NEB) calculations via the :doc:`neb ` command. +Style *spin/lbfgs* uses an orthogonal spin optimization (OSO) combined +to a limited-memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) approach +to minimize spin configurations. -Either the *spin*\ , *spin/cg* and *spin/lbfgs* styles are useful -in the context of magnetic geodesic nudged elastic band (GNEB) calculations -via the :doc:`neb/spin ` command. +See the :doc:`min/spin ` doc page for more information about +the *spin*\ , *spin/cg* and *spin/lbfgs* styles. + +Either the *quickmin*\ , *fire* and *fire/old* styles are useful in the +context of nudged elastic band (NEB) calculations via the :doc:`neb +` command. + +Either the *spin*\ , *spin/cg* and *spin/lbfgs* styles are useful in +the context of magnetic geodesic nudged elastic band (GNEB) +calculations via the :doc:`neb/spin ` command. .. note:: The damped dynamic minimizers use whatever timestep you have - defined via the :doc:`timestep ` command. Often they will - converge more quickly if you use a timestep about 10x larger than you - would normally use for dynamics simulations. + defined via the :doc:`timestep ` command. Often they + will converge more quickly if you use a timestep about 10x larger + than you would normally use for dynamics simulations. + For *fire*, the default timestep is recommended to be equal to + the one you would normally use for dynamics simulations. .. note:: - The *quickmin*\ , *fire*\ , *hftn*\ , and *cg/kk* styles do not yet - support the use of the :doc:`fix box/relax ` command or - minimizations involving the electron radius in :doc:`eFF ` - models. + The *quickmin*\ , *fire*\ , *fire/old*\ , *hftn*\ , and *cg/kk* styles do not yet + support the use of the :doc:`fix box/relax ` command + or minimizations involving the electron radius in :doc:`eFF + ` models. ---------- @@ -109,17 +125,19 @@ via the :doc:`neb/spin ` command. Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed on the :doc:`Speed packages ` doc -page. The accelerated styles take the same arguments and should +hardware, as discussed on the :doc:`Speed packages ` +doc page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with those packages. See the :doc:`Build package +` doc page for more info. You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the -:doc:`suffix ` command in your input script. +by including their suffix, or you can use the :doc:`-suffix +command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. @@ -151,15 +169,16 @@ Default .. _Sheppard: - - **(Sheppard)** Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106 (2008). See ref 1 in this paper for original reference to Qmin in Jonsson, Mills, Jacobsen. .. _Bitzek: - - **(Bitzek)** Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett, 97, 170201 (2006). + +.. _Guenole: + +**(Guenole)** Guenole, Noehring, Vaid, Houlle, Xie, Prakash, Bitzek, +Comput Mater Sci, (2020), in press (arXiv:190802038). diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst index 6caf4e0f43..16d2cf8bbf 100644 --- a/doc/src/minimize.rst +++ b/doc/src/minimize.rst @@ -52,10 +52,12 @@ or :doc:`limited timestep `. Or dynamics can be run using :doc:`fix viscous ` to impose a damping force that slowly drains all kinetic energy from the system. The :doc:`pair_style soft ` potential can be used to un-overlap atoms while running dynamics. +un-overlap atoms while running dynamics. Note that you can minimize some atoms in the system while holding the -coordinates of other atoms fixed by applying :doc:`fix setforce ` to the other atoms. See a fuller -discussion of using fixes while minimizing below. +coordinates of other atoms fixed by applying :doc:`fix setforce +` to the other atoms. See a fuller discussion of using +fixes while minimizing below. The :doc:`minimization styles ` *cg*\ , *sd*\ , and *hftn* involves an outer iteration loop which sets the search direction along @@ -68,16 +70,16 @@ be more robust than previous line searches we've tried. The backtracking method is described in Nocedal and Wright's Numerical Optimization (Procedure 3.1 on p 41). -The :doc:`minimization styles ` *quickmin* and *fire* perform -damped dynamics using an Euler integration step. Thus they require a -:doc:`timestep ` be defined. +The :doc:`minimization styles ` *quickmin*\ , *fire* and +*fire/old* perform damped dynamics using an Euler integration step. Thus +they require a :doc:`timestep ` be defined. .. note:: The damped dynamic minimizers use whatever timestep you have - defined via the :doc:`timestep ` command. Often they will - converge more quickly if you use a timestep about 10x larger than you - would normally use for dynamics simulations. + defined via the :doc:`timestep ` command. Often they + will converge more quickly if you use a timestep about 10x larger + than you would normally use for dynamics simulations. ---------- @@ -90,13 +92,15 @@ coordinates: .. image:: Eqs/min_energy.jpg :align: center -where the first term is the sum of all non-bonded :doc:`pairwise interactions ` including :doc:`long-range Coulombic interactions `, the 2nd through 5th terms are -:doc:`bond `, :doc:`angle `, -:doc:`dihedral `, and :doc:`improper ` -interactions respectively, and the last term is energy due to -:doc:`fixes ` which can act as constraints or apply force to atoms, -such as through interaction with a wall. See the discussion below about -how fix commands affect minimization. +where the first term is the sum of all non-bonded :doc:`pairwise +interactions ` including :doc:`long-range Coulombic +interactions `, the 2nd through 5th terms are :doc:`bond +`, :doc:`angle `, :doc:`dihedral +`, and :doc:`improper ` interactions +respectively, and the last term is energy due to :doc:`fixes ` +which can act as constraints or apply force to atoms, such as through +interaction with a wall. See the discussion below about how fix +commands affect minimization. The starting point for the minimization is the current configuration of the atoms. @@ -126,9 +130,9 @@ The minimization procedure stops if any of several criteria are met: .. note:: You can also use the :doc:`fix halt ` command to specify - a general criterion for exiting a minimization, that is a calculation - performed on the state of the current system, as defined by an - :doc:`equal-style variable `. + a general criterion for exiting a minimization, that is a + calculation performed on the state of the current system, as + defined by an :doc:`equal-style variable `. For the first criterion, the specified energy tolerance *etol* is unitless; it is met when the energy change between successive @@ -163,8 +167,8 @@ freedom, such as from the :doc:`fix box/relax ` command. Following minimization, a statistical summary is printed that lists which convergence criterion caused the minimizer to stop, as well as -information about the energy, force, final line search, and -iteration counts. An example is as follows: +information about the energy, force, final line search, and iteration +counts. An example is as follows: .. parsed-literal:: diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 43a4207fc1..c8c1028d3d 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -72,6 +72,7 @@ allocaters allosws AlO Alonso +alphashrink amap Amatrix AMD @@ -273,8 +274,8 @@ Bouguet Bourne boxcolor bp -bpls bpclermont +bpls br Branduardi Branicio @@ -557,6 +558,7 @@ defgrad defn deformable del +delaystep deleteIDs Dellago delocalization @@ -660,7 +662,9 @@ DRUDE dsf dsmc dt +dtgrow dtheta +dtshrink du dU Dudarev @@ -816,6 +820,7 @@ ethernet etol etot etotal +eulerimplicit Europhys ev eV @@ -958,10 +963,10 @@ Gahler gainsboro Galindo gamA -gamR gammaA gammaFactor gammaR +gamR Gan GaN ganzenmueller @@ -1053,6 +1058,7 @@ gstyle GTL Gubbins Guericke +Guenole gui Gumbsch Gunsteren @@ -1064,6 +1070,7 @@ gz gzipped Haak Hafskjold +halfstepback Halperin Halver Hamaker @@ -1124,6 +1131,7 @@ Homebrew hooke Hookean hotpink +Houlle howto Howto Hoyt @@ -1197,8 +1205,9 @@ infty inhomogeneities inhomogeneous init -initio +initialdelay initializations +initio InP inregion Institut @@ -1348,7 +1357,6 @@ kcl Kd KDevelop ke -kepler KE Keblinski keflag @@ -1356,6 +1364,7 @@ Keir Kelchner Kelkar Kemper +kepler keV Keyes Khersonskii @@ -1451,8 +1460,8 @@ lcbop ld ldfftw ldg -Lebedeva lebedeva +Lebedeva Lebold Lechman Lehoucq @@ -1715,8 +1724,8 @@ Mie Mikami Militzer Minary -Mindlin mincap +Mindlin mingw minima minimizations @@ -1957,6 +1966,7 @@ Nocedal nocite nocoeff nodeless +Noehring noforce Noid nolib @@ -2076,8 +2086,8 @@ ons OO opencl openKIM -OpenMP openmp +OpenMP openmpi opls Oppelstrup @@ -2250,6 +2260,7 @@ powderblue ppn pppm prd +Prakash pre Pre prec @@ -2283,6 +2294,7 @@ pthread pthreads ptm PTM +ptol ptr pu purdue @@ -2388,6 +2400,7 @@ reflectionstyle regoin Reinders reinit +relaxbox relink relTol remappings @@ -2687,9 +2700,9 @@ Startstep statcoul statcoulombs statvolt -stdlib stdin stdio +stdlib steelblue Stegailov Steinbach @@ -2853,6 +2866,7 @@ tlsph tmax Tmax tmd +tmin Tmin tmp tN @@ -2992,6 +3006,7 @@ uvm uwo Uzdin vacf +Vaid valent Valeriu valgrind @@ -3009,6 +3024,7 @@ Vashishta vasp vcm Vcm +vdfmax vdim vdisplace vdW @@ -3138,6 +3154,7 @@ xhi xHost Xiaohu Xiaowang +Xie xk xlat xlo @@ -3163,8 +3180,8 @@ xy xyz xz xzhou -YAFF yaff +YAFF Yamada Yazdani Ybar diff --git a/examples/fire/README b/examples/fire/README new file mode 100644 index 0000000000..da63b1a631 --- /dev/null +++ b/examples/fire/README @@ -0,0 +1,23 @@ +These examples are similar to those in the "min" and "neb" folders. +Each example can be run with the following minimization style: +- quickmin: qm +- fire: fire +- fire with optimized options: fire_mod +- fire with min_modify options to + reproduce fire/old: fire_mod_old +- fire/old (previous implementation): fire_old + +Run the NEB examples as: + +mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.qm +mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.fire +mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.fire_mod +mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.fire_mod_old +mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.fire_old + +mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.qm +mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.fire +mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.fire_mod +mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.fire_mod_old +mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.fire_old + diff --git a/examples/fire/Si.sw b/examples/fire/Si.sw new file mode 100644 index 0000000000..db4be100ef --- /dev/null +++ b/examples/fire/Si.sw @@ -0,0 +1,18 @@ +# DATE: 2007-06-11 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Stillinger and Weber, Phys Rev B, 31, 5262, (1985) +# Stillinger-Weber parameters for various elements and mixtures +# multiple entries can be added to this file, LAMMPS reads the ones it needs +# these entries are in LAMMPS "metal" units: +# epsilon = eV; sigma = Angstroms +# other quantities are unitless + +# format of a single entry (one or more lines): +# element 1, element 2, element 3, +# epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol + +# Here are the original parameters in metal units, for Silicon from: +# +# Stillinger and Weber, Phys. Rev. B, v. 31, p. 5262, (1985) +# + +Si Si Si 2.1683 2.0951 1.80 21.0 1.20 -0.333333333333 + 7.049556277 0.6022245584 4.0 0.0 0.0 diff --git a/examples/fire/final.sivac b/examples/fire/final.sivac new file mode 100644 index 0000000000..a0e2a2ed60 --- /dev/null +++ b/examples/fire/final.sivac @@ -0,0 +1,8 @@ +7 +174 6.86775 9.49992 9.62069 +175 9.46441 6.90709 9.62317 +301 6.87004 6.90631 12.2171 +304 8.44266 8.48312 11.1965 +306 10.5121 8.48457 13.2624 +331 8.44223 10.5435 13.2633 +337 10.5124 10.5437 11.1959 diff --git a/examples/fire/in.cg b/examples/fire/in.cg new file mode 100644 index 0000000000..308c7ac4ab --- /dev/null +++ b/examples/fire/in.cg @@ -0,0 +1,45 @@ +# 2d Lennard-Jones melt and subsequent energy minimization + +units lj +dimension 2 +atom_style atomic + +lattice sq2 0.8442 +region box block 0 20 0 20 -0.1 0.1 +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +velocity all create 5.0 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_modify shift yes + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +fix 2 all enforce2d + +#dump 1 all atom 100 dump.min + +#dump 2 all image 50 image.*.jpg type type & +# zoom 1.6 adiam 1.5 +#dump_modify 2 pad 4 + +#dump 3 all movie 50 movie.mpg type type & +# zoom 1.6 adiam 1.5 +#dump_modify 3 pad 4 + +thermo 100 + +run 1000 + +neigh_modify delay 0 every 1 check yes + +#dump_modify 1 every 25 + +thermo 50 +min_style cg +minimize 0.0 1.0e-6 10000 10000 diff --git a/examples/fire/in.fire b/examples/fire/in.fire new file mode 100644 index 0000000000..3a062487f3 --- /dev/null +++ b/examples/fire/in.fire @@ -0,0 +1,45 @@ +# 2d Lennard-Jones melt and subsequent energy minimization + +units lj +dimension 2 +atom_style atomic + +lattice sq2 0.8442 +region box block 0 20 0 20 -0.1 0.1 +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +velocity all create 5.0 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_modify shift yes + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +fix 2 all enforce2d + +#dump 1 all atom 100 dump.min + +#dump 2 all image 50 image.*.jpg type type & +# zoom 1.6 adiam 1.5 +#dump_modify 2 pad 4 + +#dump 3 all movie 50 movie.mpg type type & +# zoom 1.6 adiam 1.5 +#dump_modify 3 pad 4 + +thermo 100 + +run 1000 + +neigh_modify delay 0 every 1 check yes + +#dump_modify 1 every 25 + +thermo 50 +min_style fire +minimize 0.0 1.0e-6 10000 10000 diff --git a/examples/fire/in.fire_mod b/examples/fire/in.fire_mod new file mode 100644 index 0000000000..8cf0d9f48d --- /dev/null +++ b/examples/fire/in.fire_mod @@ -0,0 +1,46 @@ +# 2d Lennard-Jones melt and subsequent energy minimization + +units lj +dimension 2 +atom_style atomic + +lattice sq2 0.8442 +region box block 0 20 0 20 -0.1 0.1 +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +velocity all create 5.0 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_modify shift yes + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +fix 2 all enforce2d + +#dump 1 all atom 100 dump.min + +#dump 2 all image 50 image.*.jpg type type & +# zoom 1.6 adiam 1.5 +#dump_modify 2 pad 4 + +#dump 3 all movie 50 movie.mpg type type & +# zoom 1.6 adiam 1.5 +#dump_modify 3 pad 4 + +thermo 100 + +run 1000 + +neigh_modify delay 0 every 1 check yes + +#dump_modify 1 every 25 + +thermo 50 +min_style fire +min_modify alpha0 0.10 integrator verlet +minimize 0.0 1.0e-6 10000 10000 diff --git a/examples/fire/in.fire_mod_old b/examples/fire/in.fire_mod_old new file mode 100644 index 0000000000..b954085052 --- /dev/null +++ b/examples/fire/in.fire_mod_old @@ -0,0 +1,48 @@ +# 2d Lennard-Jones melt and subsequent energy minimization + +units lj +dimension 2 +atom_style atomic + +lattice sq2 0.8442 +region box block 0 20 0 20 -0.1 0.1 +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +velocity all create 5.0 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_modify shift yes + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +fix 2 all enforce2d + +#dump 1 all atom 100 dump.min + +#dump 2 all image 50 image.*.jpg type type & +# zoom 1.6 adiam 1.5 +#dump_modify 2 pad 4 + +#dump 3 all movie 50 movie.mpg type type & +# zoom 1.6 adiam 1.5 +#dump_modify 3 pad 4 + +thermo 100 + +run 1000 + +neigh_modify delay 0 every 1 check yes + +#dump_modify 1 every 25 + +thermo 50 +min_style fire +min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 & + dtgrow 1.1 dtshrink 0.5 alpha0 0.1 alphashrink 0.99 & + vdfmax 100000 halfstepback no initialdelay no +minimize 0.0 1.0e-6 10000 10000 diff --git a/examples/fire/in.fire_old b/examples/fire/in.fire_old new file mode 100644 index 0000000000..c25912cdee --- /dev/null +++ b/examples/fire/in.fire_old @@ -0,0 +1,45 @@ +# 2d Lennard-Jones melt and subsequent energy minimization + +units lj +dimension 2 +atom_style atomic + +lattice sq2 0.8442 +region box block 0 20 0 20 -0.1 0.1 +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +velocity all create 5.0 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_modify shift yes + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +fix 2 all enforce2d + +#dump 1 all atom 100 dump.min + +#dump 2 all image 50 image.*.jpg type type & +# zoom 1.6 adiam 1.5 +#dump_modify 2 pad 4 + +#dump 3 all movie 50 movie.mpg type type & +# zoom 1.6 adiam 1.5 +#dump_modify 3 pad 4 + +thermo 100 + +run 1000 + +neigh_modify delay 0 every 1 check yes + +#dump_modify 1 every 25 + +thermo 50 +min_style fire/old +minimize 0.0 1.0e-6 10000 10000 diff --git a/examples/fire/in.neb.sivac.fire b/examples/fire/in.neb.sivac.fire new file mode 100644 index 0000000000..36645f5c0f --- /dev/null +++ b/examples/fire/in.neb.sivac.fire @@ -0,0 +1,78 @@ +# NEB simulation of vacancy hopping in silicon crystal + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +# coordination number cutoff + +variable r equal 2.835 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a & + a1 1.0 0.0 0.0 & + a2 0.0 1.0 0.0 & + a3 0.0 0.0 1.0 & + basis 0.0 0.0 0.0 & + basis 0.0 0.5 0.5 & + basis 0.5 0.0 0.5 & + basis 0.5 0.5 0.0 & + basis 0.25 0.25 0.25 & + basis 0.25 0.75 0.75 & + basis 0.75 0.25 0.75 & + basis 0.75 0.75 0.25 + +region myreg block 0 4 & + 0 4 & + 0 4 + +#create_box 1 myreg +#create_atoms 1 region myreg +#mass 1 28.06 +#write_data initial.sivac + +read_data initial.sivac + +# make a vacancy + +group Si type 1 + +group del id 300 +delete_atoms group del compress no +group vacneigh id 174 175 301 304 306 331 337 + +# choose potential + +pair_style sw +pair_coeff * * Si.sw Si + +# set up neb run + +variable u uloop 20 + +# only output atoms near vacancy + +#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z + +# initial minimization to relax vacancy + +displace_atoms all random 0.1 0.1 0.1 123456 +minimize 1.0e-6 1.0e-4 1000 10000 + +reset_timestep 0 + +fix 1 all neb 1.0 + +thermo 100 + +# run NEB for 2000 steps or to force tolerance + +timestep 0.01 +min_style fire + +neb 0.0 0.01 100 100 10 final final.sivac diff --git a/examples/fire/in.neb.sivac.fire_mod b/examples/fire/in.neb.sivac.fire_mod new file mode 100644 index 0000000000..461bf642f1 --- /dev/null +++ b/examples/fire/in.neb.sivac.fire_mod @@ -0,0 +1,78 @@ +# NEB simulation of vacancy hopping in silicon crystal + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +# coordination number cutoff + +variable r equal 2.835 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a & + a1 1.0 0.0 0.0 & + a2 0.0 1.0 0.0 & + a3 0.0 0.0 1.0 & + basis 0.0 0.0 0.0 & + basis 0.0 0.5 0.5 & + basis 0.5 0.0 0.5 & + basis 0.5 0.5 0.0 & + basis 0.25 0.25 0.25 & + basis 0.25 0.75 0.75 & + basis 0.75 0.25 0.75 & + basis 0.75 0.75 0.25 + +region myreg block 0 4 & + 0 4 & + 0 4 + +#create_box 1 myreg +#create_atoms 1 region myreg +#mass 1 28.06 +#write_data initial.sivac + +read_data initial.sivac + +# make a vacancy + +group Si type 1 + +group del id 300 +delete_atoms group del compress no +group vacneigh id 174 175 301 304 306 331 337 + +# choose potential + +pair_style sw +pair_coeff * * Si.sw Si + +# set up neb run + +variable u uloop 20 + +# only output atoms near vacancy + +#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z + +# initial minimization to relax vacancy + +displace_atoms all random 0.1 0.1 0.1 123456 +minimize 1.0e-6 1.0e-4 1000 10000 + +reset_timestep 0 + +fix 1 all neb 1.0 + +thermo 100 + +# run NEB for 2000 steps or to force tolerance + +timestep 0.01 +min_style fire +min_modify integrator verlet +neb 0.0 0.01 100 100 10 final final.sivac diff --git a/examples/fire/in.neb.sivac.fire_mod_old b/examples/fire/in.neb.sivac.fire_mod_old new file mode 100644 index 0000000000..fba0424b74 --- /dev/null +++ b/examples/fire/in.neb.sivac.fire_mod_old @@ -0,0 +1,80 @@ +# NEB simulation of vacancy hopping in silicon crystal + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +# coordination number cutoff + +variable r equal 2.835 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a & + a1 1.0 0.0 0.0 & + a2 0.0 1.0 0.0 & + a3 0.0 0.0 1.0 & + basis 0.0 0.0 0.0 & + basis 0.0 0.5 0.5 & + basis 0.5 0.0 0.5 & + basis 0.5 0.5 0.0 & + basis 0.25 0.25 0.25 & + basis 0.25 0.75 0.75 & + basis 0.75 0.25 0.75 & + basis 0.75 0.75 0.25 + +region myreg block 0 4 & + 0 4 & + 0 4 + +#create_box 1 myreg +#create_atoms 1 region myreg +#mass 1 28.06 +#write_data initial.sivac + +read_data initial.sivac + +# make a vacancy + +group Si type 1 + +group del id 300 +delete_atoms group del compress no +group vacneigh id 174 175 301 304 306 331 337 + +# choose potential + +pair_style sw +pair_coeff * * Si.sw Si + +# set up neb run + +variable u uloop 20 + +# only output atoms near vacancy + +#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z + +# initial minimization to relax vacancy + +displace_atoms all random 0.1 0.1 0.1 123456 +minimize 1.0e-6 1.0e-4 1000 10000 + +reset_timestep 0 + +fix 1 all neb 1.0 + +thermo 100 + +# run NEB for 2000 steps or to force tolerance + +timestep 0.01 +min_style fire +min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 & + dtgrow 1.1 dtshrink 0.5 alpha0 0.1 alphashrink 0.99 & + vdfmax 100000 halfstepback no initialdelay no +neb 0.0 0.01 100 100 10 final final.sivac diff --git a/examples/fire/in.neb.sivac.fire_old b/examples/fire/in.neb.sivac.fire_old new file mode 100644 index 0000000000..64dc0fdc90 --- /dev/null +++ b/examples/fire/in.neb.sivac.fire_old @@ -0,0 +1,78 @@ +# NEB simulation of vacancy hopping in silicon crystal + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +# coordination number cutoff + +variable r equal 2.835 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a & + a1 1.0 0.0 0.0 & + a2 0.0 1.0 0.0 & + a3 0.0 0.0 1.0 & + basis 0.0 0.0 0.0 & + basis 0.0 0.5 0.5 & + basis 0.5 0.0 0.5 & + basis 0.5 0.5 0.0 & + basis 0.25 0.25 0.25 & + basis 0.25 0.75 0.75 & + basis 0.75 0.25 0.75 & + basis 0.75 0.75 0.25 + +region myreg block 0 4 & + 0 4 & + 0 4 + +#create_box 1 myreg +#create_atoms 1 region myreg +#mass 1 28.06 +#write_data initial.sivac + +read_data initial.sivac + +# make a vacancy + +group Si type 1 + +group del id 300 +delete_atoms group del compress no +group vacneigh id 174 175 301 304 306 331 337 + +# choose potential + +pair_style sw +pair_coeff * * Si.sw Si + +# set up neb run + +variable u uloop 20 + +# only output atoms near vacancy + +#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z + +# initial minimization to relax vacancy + +displace_atoms all random 0.1 0.1 0.1 123456 +minimize 1.0e-6 1.0e-4 1000 10000 + +reset_timestep 0 + +fix 1 all neb 1.0 + +thermo 100 + +# run NEB for 2000 steps or to force tolerance + +timestep 0.01 +min_style fire/old + +neb 0.0 0.01 100 100 10 final final.sivac diff --git a/examples/fire/in.neb.sivac.qm b/examples/fire/in.neb.sivac.qm new file mode 100644 index 0000000000..941d063b90 --- /dev/null +++ b/examples/fire/in.neb.sivac.qm @@ -0,0 +1,78 @@ +# NEB simulation of vacancy hopping in silicon crystal + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +# coordination number cutoff + +variable r equal 2.835 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a & + a1 1.0 0.0 0.0 & + a2 0.0 1.0 0.0 & + a3 0.0 0.0 1.0 & + basis 0.0 0.0 0.0 & + basis 0.0 0.5 0.5 & + basis 0.5 0.0 0.5 & + basis 0.5 0.5 0.0 & + basis 0.25 0.25 0.25 & + basis 0.25 0.75 0.75 & + basis 0.75 0.25 0.75 & + basis 0.75 0.75 0.25 + +region myreg block 0 4 & + 0 4 & + 0 4 + +#create_box 1 myreg +#create_atoms 1 region myreg +#mass 1 28.06 +#write_data initial.sivac + +read_data initial.sivac + +# make a vacancy + +group Si type 1 + +group del id 300 +delete_atoms group del compress no +group vacneigh id 174 175 301 304 306 331 337 + +# choose potential + +pair_style sw +pair_coeff * * Si.sw Si + +# set up neb run + +variable u uloop 20 + +# only output atoms near vacancy + +#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z + +# initial minimization to relax vacancy + +displace_atoms all random 0.1 0.1 0.1 123456 +minimize 1.0e-6 1.0e-4 1000 10000 + +reset_timestep 0 + +fix 1 all neb 1.0 + +thermo 100 + +# run NEB for 2000 steps or to force tolerance + +timestep 0.01 +min_style quickmin + +neb 0.0 0.01 100 100 10 final final.sivac diff --git a/examples/fire/initial.sivac b/examples/fire/initial.sivac new file mode 100644 index 0000000000..5664b6c39a --- /dev/null +++ b/examples/fire/initial.sivac @@ -0,0 +1,1042 @@ +LAMMPS data file via write_data, version 27 Sep 2016, timestep = 0 + +512 atoms +1 atom types + +0.0000000000000000e+00 2.1724000000000000e+01 xlo 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b/examples/fire/log.09Janv20.cg.g++.1 @@ -0,0 +1,155 @@ +LAMMPS (09 Jan 2020) +# 2d Lennard-Jones melt and subsequent energy minimization + +units lj +dimension 2 +atom_style atomic + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box block 0 20 0 20 -0.1 0.1 +create_box 1 box +Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 800 atoms + create_atoms CPU = 0.000325 secs +mass 1 1.0 + +velocity all create 5.0 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_modify shift yes + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +fix 2 all enforce2d + +#dump 1 all atom 100 dump.min + +#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5 +#dump_modify 2 pad 4 + +#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5 +#dump_modify 3 pad 4 + +thermo 100 + +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 22 22 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.057 | 3.057 | 3.057 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 5 -2.461717 0 2.532033 5.0190509 + 100 3.2788864 -0.74311698 0 2.5316708 15.912832 + 200 3.3041082 -0.77000277 0 2.5299752 15.602653 + 300 3.3840228 -0.84859211 0 2.5312006 15.188203 + 400 3.3916063 -0.85694601 0 2.5304208 15.383853 + 500 3.3136052 -0.77935263 0 2.5301106 15.833296 + 600 3.3888915 -0.85213743 0 2.532518 15.162759 + 700 3.2123675 -0.67642318 0 2.5319289 16.310565 + 800 3.3016275 -0.76569171 0 2.5318087 15.639335 + 900 3.4639203 -0.92788002 0 2.5317104 14.765912 + 1000 3.3256788 -0.79078181 0 2.5307399 15.599298 +Loop time of 0.149596 on 1 procs for 1000 steps with 800 atoms + +Performance: 2887777.748 tau/day, 6684.671 timesteps/s +98.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.092428 | 0.092428 | 0.092428 | 0.0 | 61.79 +Neigh | 0.040435 | 0.040435 | 0.040435 | 0.0 | 27.03 +Comm | 0.003456 | 0.003456 | 0.003456 | 0.0 | 2.31 +Output | 0.000191 | 0.000191 | 0.000191 | 0.0 | 0.13 +Modify | 0.009599 | 0.009599 | 0.009599 | 0.0 | 6.42 +Other | | 0.003487 | | | 2.33 + +Nlocal: 800 ave 800 max 800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 317 ave 317 max 317 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7743 ave 7743 max 7743 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7743 +Ave neighs/atom = 9.67875 +Neighbor list builds = 203 +Dangerous builds = 0 + +neigh_modify delay 0 every 1 check yes + +#dump_modify 1 every 25 + +thermo 50 +min_style cg +minimize 0.0 1.0e-6 10000 10000 +Per MPI rank memory allocation (min/avg/max) = 4.183 | 4.183 | 4.183 Mbytes +Step Temp E_pair E_mol TotEng Press + 1000 3.3256788 -0.79078181 0 2.5307399 15.599298 + 1050 3.3256788 -2.8361415 0 0.48538014 1.6090001 + 1100 3.3256788 -2.8661626 0 0.45535906 1.6175322 + 1150 3.3256788 -2.8783275 0 0.44319421 1.6293715 + 1200 3.3256788 -2.8838202 0 0.43770144 1.6393211 + 1250 3.3256788 -2.8956657 0 0.42585599 1.604841 + 1300 3.3256788 -2.9039122 0 0.41760945 1.6594733 + 1350 3.3256788 -2.9100776 0 0.4114441 1.7004165 + 1400 3.3256788 -2.9131297 0 0.40839199 1.7078217 + 1450 3.3256788 -2.9167506 0 0.40477104 1.7780477 + 1500 3.3256788 -2.916974 0 0.4045477 1.7981449 + 1550 3.3256788 -2.9169794 0 0.40454227 1.8023577 + 1600 3.3256788 -2.9169795 0 0.40454213 1.8030228 + 1650 3.3256788 -2.9169795 0 0.40454213 1.8030432 + 1700 3.3256788 -2.9169795 0 0.40454213 1.8030396 + 1750 3.3256788 -2.9169795 0 0.40454213 1.8030394 + 1800 3.3256788 -2.9169795 0 0.40454213 1.8030395 + 1803 3.3256788 -2.9169795 0 0.40454213 1.8030395 +Loop time of 0.293121 on 1 procs for 803 steps with 800 atoms + +98.8% CPU use with 1 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = force tolerance + Energy initial, next-to-last, final = + -0.790781812776 -2.91697954354 -2.91697954354 + Force two-norm initial, final = 1905.47 9.82516e-07 + Force max component initial, final = 343.392 3.01878e-07 + Final line search alpha, max atom move = 1 3.01878e-07 + Iterations, force evaluations = 803 1596 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.24243 | 0.24243 | 0.24243 | 0.0 | 82.71 +Neigh | 0.016566 | 0.016566 | 0.016566 | 0.0 | 5.65 +Comm | 0.00342 | 0.00342 | 0.00342 | 0.0 | 1.17 +Output | 0.000318 | 0.000318 | 0.000318 | 0.0 | 0.11 +Modify | 0.005032 | 0.005032 | 0.005032 | 0.0 | 1.72 +Other | | 0.02536 | | | 8.65 + +Nlocal: 800 ave 800 max 800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 329 ave 329 max 329 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 6957 ave 6957 max 6957 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 6957 +Ave neighs/atom = 8.69625 +Neighbor list builds = 85 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/fire/log.09Janv20.fire.g++.1 b/examples/fire/log.09Janv20.fire.g++.1 new file mode 100644 index 0000000000..d3ed3e7492 --- /dev/null +++ b/examples/fire/log.09Janv20.fire.g++.1 @@ -0,0 +1,172 @@ +LAMMPS (09 Jan 2020) +# 2d Lennard-Jones melt and subsequent energy minimization + +units lj +dimension 2 +atom_style atomic + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box block 0 20 0 20 -0.1 0.1 +create_box 1 box +Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 800 atoms + create_atoms CPU = 0.00032 secs +mass 1 1.0 + +velocity all create 5.0 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_modify shift yes + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +fix 2 all enforce2d + +#dump 1 all atom 100 dump.min + +#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5 +#dump_modify 2 pad 4 + +#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5 +#dump_modify 3 pad 4 + +thermo 100 + +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 22 22 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.057 | 3.057 | 3.057 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 5 -2.461717 0 2.532033 5.0190509 + 100 3.2788864 -0.74311698 0 2.5316708 15.912832 + 200 3.3041082 -0.77000277 0 2.5299752 15.602653 + 300 3.3840228 -0.84859211 0 2.5312006 15.188203 + 400 3.3916063 -0.85694601 0 2.5304208 15.383853 + 500 3.3136052 -0.77935263 0 2.5301106 15.833296 + 600 3.3888915 -0.85213743 0 2.532518 15.162759 + 700 3.2123675 -0.67642318 0 2.5319289 16.310565 + 800 3.3016275 -0.76569171 0 2.5318087 15.639335 + 900 3.4639203 -0.92788002 0 2.5317104 14.765912 + 1000 3.3256788 -0.79078181 0 2.5307399 15.599298 +Loop time of 0.148541 on 1 procs for 1000 steps with 800 atoms + +Performance: 2908287.947 tau/day, 6732.148 timesteps/s +99.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.090497 | 0.090497 | 0.090497 | 0.0 | 60.92 +Neigh | 0.041085 | 0.041085 | 0.041085 | 0.0 | 27.66 +Comm | 0.003431 | 0.003431 | 0.003431 | 0.0 | 2.31 +Output | 0.000188 | 0.000188 | 0.000188 | 0.0 | 0.13 +Modify | 0.009931 | 0.009931 | 0.009931 | 0.0 | 6.69 +Other | | 0.003409 | | | 2.29 + +Nlocal: 800 ave 800 max 800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 317 ave 317 max 317 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7743 ave 7743 max 7743 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7743 +Ave neighs/atom = 9.67875 +Neighbor list builds = 203 +Dangerous builds = 0 + +neigh_modify delay 0 every 1 check yes + +#dump_modify 1 every 25 + +thermo 50 +min_style fire +minimize 0.0 1.0e-6 10000 10000 + Parameters for fire: + dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback relaxbox relaxbox_mod relaxbox_rate ptol + 0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes +Per MPI rank memory allocation (min/avg/max) = 3.058 | 3.058 | 3.058 Mbytes +Step Temp E_pair E_mol TotEng Press + 1000 0 -0.79078181 0 -0.79078181 12.79527 + 1050 0.026844171 -2.7795211 0 -2.7527105 -0.87603277 + 1100 0.0034822073 -2.8529023 0 -2.8494245 -1.2124257 + 1150 0.00086547466 -2.868953 0 -2.8680886 -1.2359795 + 1200 0.00097619081 -2.8772187 0 -2.8762437 -1.286455 + 1250 0.0010932112 -2.8815244 0 -2.8804326 -1.3030012 + 1300 0.00011570361 -2.8827401 0 -2.8826246 -1.3040874 + 1350 0.00013328904 -2.8829838 0 -2.8828506 -1.2996017 + 1400 0.00018991693 -2.8844011 0 -2.8842114 -1.2697602 + 1450 0.0017139171 -2.8880702 0 -2.8863584 -1.2367621 + 1500 0.00015838581 -2.891362 0 -2.8912038 -1.1688764 + 1550 3.671122e-05 -2.8920253 0 -2.8919886 -1.1669644 + 1600 8.5025973e-05 -2.8924697 0 -2.8923848 -1.1565595 + 1650 0.00031059668 -2.8932768 0 -2.8929666 -1.1412709 + 1700 8.5903751e-05 -2.8936767 0 -2.8935909 -1.1287456 + 1750 5.1139269e-08 -2.8937466 0 -2.8937466 -1.1280269 + 1800 1.1671203e-07 -2.893751 0 -2.8937509 -1.1269919 + 1850 1.6442171e-07 -2.8937533 0 -2.8937532 -1.1269835 + 1900 2.7880101e-06 -2.8937574 0 -2.8937546 -1.128914 + 1950 9.7931277e-05 -2.8948559 0 -2.894758 -1.1298435 + 2000 8.8954569e-06 -2.8948879 0 -2.894879 -1.1291332 + 2050 1.3956548e-06 -2.8949028 0 -2.8949014 -1.1286287 + 2100 4.250297e-07 -2.8949058 0 -2.8949054 -1.1286873 + 2150 7.8744547e-08 -2.8949064 0 -2.8949063 -1.128789 + 2200 6.1147167e-10 -2.8949064 0 -2.8949064 -1.1288611 + 2250 3.0004658e-10 -2.8949064 0 -2.8949064 -1.1288707 + 2300 1.2118076e-10 -2.8949064 0 -2.8949064 -1.1288784 + 2350 9.1550426e-12 -2.8949064 0 -2.8949064 -1.128882 + 2400 2.7467472e-14 -2.8949064 0 -2.8949064 -1.1288819 + 2450 1.8628857e-14 -2.8949064 0 -2.8949064 -1.1288818 + 2500 6.6730826e-15 -2.8949064 0 -2.8949064 -1.1288818 + 2532 1.4818811e-15 -2.8949064 0 -2.8949064 -1.1288817 +Loop time of 0.281178 on 1 procs for 1532 steps with 800 atoms + +98.4% CPU use with 1 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = force tolerance + Energy initial, next-to-last, final = + -0.790781812776 -2.89490640353 -2.89490640353 + Force two-norm initial, final = 1905.47 9.86158e-07 + Force max component initial, final = 343.392 6.07974e-07 + Final line search alpha, max atom move = 0 0 + Iterations, force evaluations = 1532 1532 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.23639 | 0.23639 | 0.23639 | 0.0 | 84.07 +Neigh | 0.011136 | 0.011136 | 0.011136 | 0.0 | 3.96 +Comm | 0.003118 | 0.003118 | 0.003118 | 0.0 | 1.11 +Output | 0.000591 | 0.000591 | 0.000591 | 0.0 | 0.21 +Modify | 0.004883 | 0.004883 | 0.004883 | 0.0 | 1.74 +Other | | 0.02506 | | | 8.91 + +Nlocal: 800 ave 800 max 800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 327 ave 327 max 327 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7012 ave 7012 max 7012 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7012 +Ave neighs/atom = 8.765 +Neighbor list builds = 55 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/fire/log.09Janv20.fire_mod.g++.1 b/examples/fire/log.09Janv20.fire_mod.g++.1 new file mode 100644 index 0000000000..69a23648ab --- /dev/null +++ b/examples/fire/log.09Janv20.fire_mod.g++.1 @@ -0,0 +1,161 @@ +LAMMPS (09 Jan 2020) +# 2d Lennard-Jones melt and subsequent energy minimization + +units lj +dimension 2 +atom_style atomic + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box block 0 20 0 20 -0.1 0.1 +create_box 1 box +Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 800 atoms + create_atoms CPU = 0.000379 secs +mass 1 1.0 + +velocity all create 5.0 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_modify shift yes + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +fix 2 all enforce2d + +#dump 1 all atom 100 dump.min + +#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5 +#dump_modify 2 pad 4 + +#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5 +#dump_modify 3 pad 4 + +thermo 100 + +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 22 22 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.057 | 3.057 | 3.057 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 5 -2.461717 0 2.532033 5.0190509 + 100 3.2788864 -0.74311698 0 2.5316708 15.912832 + 200 3.3041082 -0.77000277 0 2.5299752 15.602653 + 300 3.3840228 -0.84859211 0 2.5312006 15.188203 + 400 3.3916063 -0.85694601 0 2.5304208 15.383853 + 500 3.3136052 -0.77935263 0 2.5301106 15.833296 + 600 3.3888915 -0.85213743 0 2.532518 15.162759 + 700 3.2123675 -0.67642318 0 2.5319289 16.310565 + 800 3.3016275 -0.76569171 0 2.5318087 15.639335 + 900 3.4639203 -0.92788002 0 2.5317104 14.765912 + 1000 3.3256788 -0.79078181 0 2.5307399 15.599298 +Loop time of 0.15409 on 1 procs for 1000 steps with 800 atoms + +Performance: 2803556.363 tau/day, 6489.714 timesteps/s +97.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.094416 | 0.094416 | 0.094416 | 0.0 | 61.27 +Neigh | 0.041223 | 0.041223 | 0.041223 | 0.0 | 26.75 +Comm | 0.003956 | 0.003956 | 0.003956 | 0.0 | 2.57 +Output | 0.000253 | 0.000253 | 0.000253 | 0.0 | 0.16 +Modify | 0.010146 | 0.010146 | 0.010146 | 0.0 | 6.58 +Other | | 0.004096 | | | 2.66 + +Nlocal: 800 ave 800 max 800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 317 ave 317 max 317 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7743 ave 7743 max 7743 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7743 +Ave neighs/atom = 9.67875 +Neighbor list builds = 203 +Dangerous builds = 0 + +neigh_modify delay 0 every 1 check yes + +#dump_modify 1 every 25 + +thermo 50 +min_style fire +min_modify alpha0 0.10 integrator verlet +minimize 0.0 1.0e-6 10000 10000 + Parameters for fire: + dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback relaxbox relaxbox_mod relaxbox_rate ptol + 0.1 20 1.1 0.5 0.1 0.99 10 0.02 verlet yes +Per MPI rank memory allocation (min/avg/max) = 3.058 | 3.058 | 3.058 Mbytes +Step Temp E_pair E_mol TotEng Press + 1000 0 -0.79078181 0 -0.79078181 12.79527 + 1050 0.078268931 -2.7183168 0 -2.6401457 -0.41989487 + 1100 0.004111801 -2.8430419 0 -2.8389353 -1.3043522 + 1150 0.005000915 -2.8768555 0 -2.8718608 -1.2706615 + 1200 0.00221302 -2.8879134 0 -2.8857032 -1.2778479 + 1250 0.00043036592 -2.8939906 0 -2.8935608 -1.268974 + 1300 0.0014677683 -2.8992098 0 -2.8977439 -1.2905094 + 1350 0.00093281043 -2.9019313 0 -2.9009996 -1.2653586 + 1400 0.0005425017 -2.9060403 0 -2.9054984 -1.2368252 + 1450 6.0662419e-05 -2.9065294 0 -2.9064688 -1.2376477 + 1500 3.8768552e-05 -2.9066587 0 -2.9066199 -1.2235528 + 1550 4.8205498e-06 -2.9066767 0 -2.9066719 -1.2267388 + 1600 3.7010898e-07 -2.9066803 0 -2.90668 -1.2280952 + 1650 9.3344403e-09 -2.9066807 0 -2.9066806 -1.22862 + 1700 3.595307e-09 -2.9066807 0 -2.9066807 -1.2285492 + 1750 2.7152688e-11 -2.9066807 0 -2.9066807 -1.2285418 + 1800 2.9643465e-12 -2.9066807 0 -2.9066807 -1.2285402 + 1850 8.8599324e-15 -2.9066807 0 -2.9066807 -1.2285389 + 1900 8.1537037e-15 -2.9066807 0 -2.9066807 -1.2285389 + 1919 1.8744314e-15 -2.9066807 0 -2.9066807 -1.2285389 +Loop time of 0.172896 on 1 procs for 919 steps with 800 atoms + +98.8% CPU use with 1 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = force tolerance + Energy initial, next-to-last, final = + -0.790781812776 -2.90668068533 -2.90668068533 + Force two-norm initial, final = 1905.47 9.38529e-07 + Force max component initial, final = 343.392 2.3828e-07 + Final line search alpha, max atom move = 0 0 + Iterations, force evaluations = 919 919 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.14136 | 0.14136 | 0.14136 | 0.0 | 81.76 +Neigh | 0.009759 | 0.009759 | 0.009759 | 0.0 | 5.64 +Comm | 0.001941 | 0.001941 | 0.001941 | 0.0 | 1.12 +Output | 0.000313 | 0.000313 | 0.000313 | 0.0 | 0.18 +Modify | 0.002814 | 0.002814 | 0.002814 | 0.0 | 1.63 +Other | | 0.01671 | | | 9.66 + +Nlocal: 800 ave 800 max 800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 320 ave 320 max 320 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7003 ave 7003 max 7003 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7003 +Ave neighs/atom = 8.75375 +Neighbor list builds = 51 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/fire/log.09Janv20.fire_mod_old.g++.1 b/examples/fire/log.09Janv20.fire_mod_old.g++.1 new file mode 100644 index 0000000000..3cd1fbd386 --- /dev/null +++ b/examples/fire/log.09Janv20.fire_mod_old.g++.1 @@ -0,0 +1,342 @@ +LAMMPS (09 Jan 2020) +# 2d Lennard-Jones melt and subsequent energy minimization + +units lj +dimension 2 +atom_style atomic + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box block 0 20 0 20 -0.1 0.1 +create_box 1 box +Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 800 atoms + create_atoms CPU = 0.000356 secs +mass 1 1.0 + +velocity all create 5.0 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_modify shift yes + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +fix 2 all enforce2d + +#dump 1 all atom 100 dump.min + +#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5 +#dump_modify 2 pad 4 + +#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5 +#dump_modify 3 pad 4 + +thermo 100 + +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 22 22 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.057 | 3.057 | 3.057 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 5 -2.461717 0 2.532033 5.0190509 + 100 3.2788864 -0.74311698 0 2.5316708 15.912832 + 200 3.3041082 -0.77000277 0 2.5299752 15.602653 + 300 3.3840228 -0.84859211 0 2.5312006 15.188203 + 400 3.3916063 -0.85694601 0 2.5304208 15.383853 + 500 3.3136052 -0.77935263 0 2.5301106 15.833296 + 600 3.3888915 -0.85213743 0 2.532518 15.162759 + 700 3.2123675 -0.67642318 0 2.5319289 16.310565 + 800 3.3016275 -0.76569171 0 2.5318087 15.639335 + 900 3.4639203 -0.92788002 0 2.5317104 14.765912 + 1000 3.3256788 -0.79078181 0 2.5307399 15.599298 +Loop time of 0.149746 on 1 procs for 1000 steps with 800 atoms + +Performance: 2884885.072 tau/day, 6677.975 timesteps/s +98.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.091667 | 0.091667 | 0.091667 | 0.0 | 61.21 +Neigh | 0.041479 | 0.041479 | 0.041479 | 0.0 | 27.70 +Comm | 0.003516 | 0.003516 | 0.003516 | 0.0 | 2.35 +Output | 0.0002 | 0.0002 | 0.0002 | 0.0 | 0.13 +Modify | 0.009484 | 0.009484 | 0.009484 | 0.0 | 6.33 +Other | | 0.0034 | | | 2.27 + +Nlocal: 800 ave 800 max 800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 317 ave 317 max 317 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7743 ave 7743 max 7743 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7743 +Ave neighs/atom = 9.67875 +Neighbor list builds = 203 +Dangerous builds = 0 + +neigh_modify delay 0 every 1 check yes + +#dump_modify 1 every 25 + +thermo 50 +min_style fire +min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 dtgrow 1.1 dtshrink 0.5 alpha0 0.1 alphashrink 0.99 vdfmax 100000 halfstepback no initialdelay no +minimize 0.0 1.0e-6 10000 10000 + Parameters for fire: + dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback relaxbox relaxbox_mod relaxbox_rate ptol + 0.1 5 1.1 0.5 0.1 0.99 10 0 eulerexplicit no +Per MPI rank memory allocation (min/avg/max) = 3.058 | 3.058 | 3.058 Mbytes +Step Temp E_pair E_mol TotEng Press + 1000 0 -0.79078181 0 -0.79078181 12.79527 + 1050 0.13353902 -2.5912638 0 -2.4578917 0.5692337 + 1100 0.0089379263 -2.6989463 0 -2.6900196 -0.32199212 + 1150 0.0046843921 -2.759845 0 -2.7551664 -0.7652834 + 1200 0.002846537 -2.789411 0 -2.7865681 -0.96589949 + 1250 0.0010217747 -2.8074831 0 -2.8064626 -1.0829009 + 1300 0.0053781523 -2.8242492 0 -2.8188778 -1.1318106 + 1350 0.00023994777 -2.8341342 0 -2.8338945 -1.163692 + 1400 0.0017009757 -2.840995 0 -2.8392962 -1.16188 + 1450 0.00056400841 -2.8453557 0 -2.8447924 -1.1520067 + 1500 0.00077934345 -2.8479194 0 -2.847141 -1.154398 + 1550 0.00036611219 -2.8514157 0 -2.8510501 -1.172244 + 1600 8.9292311e-06 -2.8527434 0 -2.8527345 -1.1747761 + 1650 1.5128835e-06 -2.8542463 0 -2.8542448 -1.1844146 + 1700 3.204798e-06 -2.855907 0 -2.8559038 -1.1947962 + 1750 0.00074224769 -2.8571164 0 -2.8563751 -1.1985933 + 1800 0.00019536702 -2.8588894 0 -2.8586943 -1.2088321 + 1850 9.7569763e-05 -2.8594962 0 -2.8593988 -1.2118745 + 1900 5.7320544e-05 -2.8602172 0 -2.86016 -1.2102157 + 1950 4.5526736e-05 -2.8607722 0 -2.8607267 -1.2106069 + 2000 2.723482e-05 -2.8615425 0 -2.8615153 -1.2116304 + 2050 0.00058266182 -2.862351 0 -2.8617691 -1.2144959 + 2100 6.500145e-05 -2.8634861 0 -2.8634212 -1.2196925 + 2150 7.018255e-05 -2.8659666 0 -2.8658965 -1.2281308 + 2200 2.7358137e-05 -2.8670193 0 -2.866992 -1.2249437 + 2250 4.0619564e-05 -2.8677954 0 -2.8677549 -1.2264181 + 2300 0.00037079927 -2.869037 0 -2.8686666 -1.2228396 + 2350 1.7039984e-05 -2.8697054 0 -2.8696884 -1.2193694 + 2400 1.1706376e-05 -2.8704557 0 -2.870444 -1.2151924 + 2450 1.569166e-05 -2.8710048 0 -2.8709891 -1.2116495 + 2500 1.0764974e-05 -2.8713737 0 -2.8713629 -1.2095378 + 2550 0.00020637438 -2.8718339 0 -2.8716277 -1.2073921 + 2600 1.3281629e-05 -2.8721042 0 -2.8720909 -1.2072822 + 2650 1.6997328e-05 -2.8725439 0 -2.8725269 -1.2078205 + 2700 0.00024308504 -2.8734078 0 -2.873165 -1.2083205 + 2750 1.9325652e-05 -2.8742725 0 -2.8742532 -1.2086037 + 2800 0.00041115503 -2.8753309 0 -2.8749202 -1.2099241 + 2850 0.00016124812 -2.8763004 0 -2.8761394 -1.2100234 + 2900 0.00010261801 -2.8769077 0 -2.8768052 -1.2095838 + 2950 8.5284152e-05 -2.8773786 0 -2.8772935 -1.20663 + 3000 3.6509277e-07 -2.8779105 0 -2.8779102 -1.2054539 + 3050 0.00043346474 -2.8786802 0 -2.8782473 -1.2002574 + 3100 5.5020715e-05 -2.8790024 0 -2.8789474 -1.1951741 + 3150 2.1984131e-05 -2.8794335 0 -2.8794115 -1.1862473 + 3200 1.6745891e-05 -2.8795341 0 -2.8795174 -1.1857447 + 3250 6.7600713e-06 -2.8797504 0 -2.8797436 -1.1851768 + 3300 2.5404023e-05 -2.8799202 0 -2.8798949 -1.1853619 + 3350 1.4307979e-07 -2.8800767 0 -2.8800766 -1.1855388 + 3400 2.3771289e-05 -2.8802876 0 -2.8802639 -1.1853283 + 3450 1.5926609e-05 -2.8811779 0 -2.881162 -1.1832155 + 3500 0.00023918123 -2.8816592 0 -2.8814203 -1.1795992 + 3550 2.1477822e-05 -2.8818075 0 -2.881786 -1.1764183 + 3600 2.4171891e-06 -2.8818685 0 -2.8818661 -1.1752634 + 3650 5.1078051e-06 -2.8820201 0 -2.882015 -1.1735854 + 3700 2.8288283e-06 -2.8820776 0 -2.8820748 -1.1736177 + 3750 2.8261894e-05 -2.8821692 0 -2.882141 -1.1739042 + 3800 2.1722286e-05 -2.8823134 0 -2.8822917 -1.174473 + 3850 2.269858e-05 -2.8824364 0 -2.8824137 -1.174537 + 3900 1.6463034e-06 -2.8825758 0 -2.8825741 -1.1738041 + 3950 1.8888587e-05 -2.8827475 0 -2.8827287 -1.1730456 + 4000 7.7137595e-07 -2.8829271 0 -2.8829263 -1.1737585 + 4050 8.0218395e-06 -2.8831189 0 -2.8831108 -1.1748314 + 4100 2.1775628e-07 -2.8831738 0 -2.8831736 -1.1751807 + 4150 7.0972401e-06 -2.8832308 0 -2.8832237 -1.1756641 + 4200 4.1552084e-07 -2.8833365 0 -2.8833361 -1.1766505 + 4250 6.955018e-06 -2.8833891 0 -2.8833822 -1.1770815 + 4300 0.00016095054 -2.8835126 0 -2.8833519 -1.1780786 + 4350 6.2109296e-08 -2.8836037 0 -2.8836036 -1.1788493 + 4400 4.9552761e-05 -2.8838275 0 -2.883778 -1.1796751 + 4450 4.1572651e-06 -2.8840252 0 -2.884021 -1.1797244 + 4500 4.5094019e-05 -2.8841528 0 -2.8841078 -1.1793634 + 4550 1.5486277e-06 -2.8843566 0 -2.884355 -1.1786658 + 4600 3.124141e-06 -2.8845241 0 -2.884521 -1.1782676 + 4650 2.6550727e-06 -2.8847548 0 -2.8847521 -1.1761931 + 4700 4.1414628e-05 -2.8849662 0 -2.8849249 -1.1718684 + 4750 2.380964e-06 -2.8851283 0 -2.8851259 -1.1692959 + 4800 8.590119e-06 -2.8852449 0 -2.8852364 -1.1685065 + 4850 2.2696517e-05 -2.8854127 0 -2.88539 -1.168484 + 4900 2.5100677e-05 -2.8855573 0 -2.8855322 -1.1680468 + 4950 1.0901958e-05 -2.8857056 0 -2.8856947 -1.1667983 + 5000 1.7660672e-05 -2.8858561 0 -2.8858385 -1.1659289 + 5050 2.2115169e-05 -2.886002 0 -2.8859799 -1.1652871 + 5100 6.6278908e-05 -2.8861968 0 -2.8861306 -1.1648902 + 5150 6.0993884e-07 -2.8862934 0 -2.8862928 -1.1650736 + 5200 0.00020333351 -2.8864792 0 -2.8862761 -1.1684121 + 5250 0.00018260896 -2.8869006 0 -2.8867182 -1.1738451 + 5300 5.9589204e-06 -2.8870944 0 -2.8870884 -1.1742236 + 5350 3.9611705e-06 -2.8871855 0 -2.8871815 -1.1739438 + 5400 1.6390307e-05 -2.8872444 0 -2.8872281 -1.1738633 + 5450 1.0471949e-06 -2.8872779 0 -2.8872769 -1.173992 + 5500 3.189532e-07 -2.8873146 0 -2.8873143 -1.1745333 + 5550 8.5416909e-08 -2.8873521 0 -2.8873521 -1.1754741 + 5600 2.8826987e-06 -2.8873622 0 -2.8873594 -1.1757461 + 5650 1.4702624e-06 -2.8873706 0 -2.8873692 -1.1760765 + 5700 1.569283e-07 -2.887379 0 -2.8873788 -1.1765 + 5750 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-2.8879584 -1.1721637 + 10250 3.7458971e-12 -2.8879584 0 -2.8879584 -1.1721631 + 10300 1.285673e-13 -2.8879584 0 -2.8879584 -1.1721621 + 10350 4.5812377e-15 -2.8879584 0 -2.8879584 -1.1721611 + 10400 2.1117455e-14 -2.8879584 0 -2.8879584 -1.1721603 + 10450 8.2667409e-13 -2.8879584 0 -2.8879584 -1.17216 + 10500 2.6385234e-13 -2.8879584 0 -2.8879584 -1.1721596 + 10550 1.5919509e-13 -2.8879584 0 -2.8879584 -1.1721592 + 10600 1.9165062e-13 -2.8879584 0 -2.8879584 -1.172159 + 10650 1.3972041e-13 -2.8879584 0 -2.8879584 -1.1721583 + 10700 1.3469994e-13 -2.8879584 0 -2.8879584 -1.172158 + 10750 7.4707625e-14 -2.8879584 0 -2.8879584 -1.1721577 + 10800 7.9795578e-14 -2.8879584 0 -2.8879584 -1.1721575 + 10850 7.3860559e-13 -2.8879584 0 -2.8879584 -1.1721572 + 10900 9.8555453e-13 -2.8879584 0 -2.8879584 -1.1721569 + 10950 3.487218e-15 -2.8879584 0 -2.8879584 -1.1721564 + 11000 1.4915771e-12 -2.8879584 0 -2.8879584 -1.172156 +Loop time of 1.75996 on 1 procs for 10000 steps with 800 atoms + +98.4% CPU use with 1 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = max iterations + Energy initial, next-to-last, final = + -0.790781812776 -2.88795843023 -2.88795843023 + Force two-norm initial, final = 1905.47 9.60915e-05 + Force max component initial, final = 343.392 3.71774e-05 + Final line search alpha, max atom move = 0 0 + Iterations, force evaluations = 10000 10000 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.5377 | 1.5377 | 1.5377 | 0.0 | 87.37 +Neigh | 0.012664 | 0.012664 | 0.012664 | 0.0 | 0.72 +Comm | 0.015656 | 0.015656 | 0.015656 | 0.0 | 0.89 +Output | 0.004186 | 0.004186 | 0.004186 | 0.0 | 0.24 +Modify | 0.02968 | 0.02968 | 0.02968 | 0.0 | 1.69 +Other | | 0.16 | | | 9.09 + +Nlocal: 800 ave 800 max 800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 311 ave 311 max 311 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7009 ave 7009 max 7009 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7009 +Ave neighs/atom = 8.76125 +Neighbor list builds = 66 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/fire/log.09Janv20.fire_old.g++.1 b/examples/fire/log.09Janv20.fire_old.g++.1 new file mode 100644 index 0000000000..863558645b --- /dev/null +++ b/examples/fire/log.09Janv20.fire_old.g++.1 @@ -0,0 +1,338 @@ +LAMMPS (09 Jan 2020) +# 2d Lennard-Jones melt and subsequent energy minimization + +units lj +dimension 2 +atom_style atomic + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box block 0 20 0 20 -0.1 0.1 +create_box 1 box +Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 800 atoms + create_atoms CPU = 0.000345 secs +mass 1 1.0 + +velocity all create 5.0 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_modify shift yes + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +fix 2 all enforce2d + +#dump 1 all atom 100 dump.min + +#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5 +#dump_modify 2 pad 4 + +#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5 +#dump_modify 3 pad 4 + +thermo 100 + +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 22 22 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.057 | 3.057 | 3.057 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 5 -2.461717 0 2.532033 5.0190509 + 100 3.2788864 -0.74311698 0 2.5316708 15.912832 + 200 3.3041082 -0.77000277 0 2.5299752 15.602653 + 300 3.3840228 -0.84859211 0 2.5312006 15.188203 + 400 3.3916063 -0.85694601 0 2.5304208 15.383853 + 500 3.3136052 -0.77935263 0 2.5301106 15.833296 + 600 3.3888915 -0.85213743 0 2.532518 15.162759 + 700 3.2123675 -0.67642318 0 2.5319289 16.310565 + 800 3.3016275 -0.76569171 0 2.5318087 15.639335 + 900 3.4639203 -0.92788002 0 2.5317104 14.765912 + 1000 3.3256788 -0.79078181 0 2.5307399 15.599298 +Loop time of 0.14894 on 1 procs for 1000 steps with 800 atoms + +Performance: 2900496.844 tau/day, 6714.113 timesteps/s +99.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.091005 | 0.091005 | 0.091005 | 0.0 | 61.10 +Neigh | 0.040404 | 0.040404 | 0.040404 | 0.0 | 27.13 +Comm | 0.003588 | 0.003588 | 0.003588 | 0.0 | 2.41 +Output | 0.000226 | 0.000226 | 0.000226 | 0.0 | 0.15 +Modify | 0.010077 | 0.010077 | 0.010077 | 0.0 | 6.77 +Other | | 0.00364 | | | 2.44 + +Nlocal: 800 ave 800 max 800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 317 ave 317 max 317 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7743 ave 7743 max 7743 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7743 +Ave neighs/atom = 9.67875 +Neighbor list builds = 203 +Dangerous builds = 0 + +neigh_modify delay 0 every 1 check yes + +#dump_modify 1 every 25 + +thermo 50 +min_style fire/old +minimize 0.0 1.0e-6 10000 10000 +Per MPI rank memory allocation (min/avg/max) = 3.058 | 3.058 | 3.058 Mbytes +Step Temp E_pair E_mol TotEng Press + 1000 0 -0.79078181 0 -0.79078181 12.79527 + 1050 0.15078629 -2.5003801 0 -2.3497823 1.2721061 + 1100 0.00074837835 -2.7050909 0 -2.7043434 -0.37905868 + 1150 0.0063037865 -2.7509932 0 -2.7446973 -0.71482554 + 1200 0.00034408524 -2.7960993 0 -2.7957557 -1.0263545 + 1250 0.00085176575 -2.8126463 0 -2.8117956 -1.1021125 + 1300 0.00033628622 -2.8280448 0 -2.8277089 -1.1471915 + 1350 0.00026177536 -2.8357089 0 -2.8354474 -1.1676514 + 1400 0.0011622998 -2.8431054 0 -2.8419446 -1.1596473 + 1450 0.0010839093 -2.8457268 0 -2.8446442 -1.1518499 + 1500 0.00024665053 -2.8480136 0 -2.8477672 -1.1520869 + 1550 7.831216e-05 -2.849584 0 -2.8495057 -1.1506084 + 1600 3.2759808e-05 -2.8511231 0 -2.8510904 -1.1497061 + 1650 3.9272607e-05 -2.8526234 0 -2.8525841 -1.1511215 + 1700 5.5569128e-05 -2.8538287 0 -2.8537732 -1.1497192 + 1750 7.4734101e-05 -2.8558245 0 -2.8557498 -1.1480928 + 1800 5.8181251e-05 -2.8575248 0 -2.8574667 -1.1518976 + 1850 2.7589109e-05 -2.8585475 0 -2.85852 -1.1511439 + 1900 0.00024942163 -2.8595367 0 -2.8592876 -1.1467285 + 1950 0.00015592998 -2.8607519 0 -2.8605962 -1.1436241 + 2000 0.00028229354 -2.8619889 0 -2.861707 -1.1439985 + 2050 0.00024971806 -2.8634866 0 -2.8632372 -1.1509204 + 2100 0.00021986576 -2.8646023 0 -2.8643827 -1.1564575 + 2150 0.00011079739 -2.8664318 0 -2.8663211 -1.1525135 + 2200 4.968224e-05 -2.8676285 0 -2.8675789 -1.1577511 + 2250 0.00072993169 -2.8690151 0 -2.868286 -1.1626387 + 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0 -2.894891 -1.1819669 + 10400 2.8045001e-05 -2.8954967 0 -2.8954687 -1.1834846 + 10450 1.1453554e-05 -2.8956053 0 -2.8955939 -1.1848261 + 10500 3.3687864e-06 -2.8956525 0 -2.8956491 -1.1850246 + 10550 1.9367666e-06 -2.8956863 0 -2.8956844 -1.1846614 + 10600 1.2782114e-07 -2.8956995 0 -2.8956994 -1.1843742 + 10650 6.6195319e-07 -2.8957052 0 -2.8957045 -1.1841825 + 10700 4.7437869e-07 -2.8957078 0 -2.8957074 -1.1840626 + 10750 1.7270059e-07 -2.8957124 0 -2.8957122 -1.1840153 + 10800 1.1015125e-07 -2.8957137 0 -2.8957136 -1.1839328 + 10850 7.0349976e-08 -2.8957147 0 -2.8957146 -1.1838699 + 10900 6.837958e-08 -2.8957152 0 -2.8957151 -1.1838349 + 10950 6.4194728e-08 -2.8957156 0 -2.8957156 -1.1838001 + 11000 4.9879507e-08 -2.8957159 0 -2.8957158 -1.1837799 +Loop time of 1.74349 on 1 procs for 10000 steps with 800 atoms + +98.3% CPU use with 1 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = max iterations + Energy initial, next-to-last, final = + -0.790781812776 -2.89571584656 -2.89571585284 + Force two-norm initial, final = 1905.47 0.0695855 + Force max component initial, final = 343.392 0.0295536 + Final line search alpha, max atom move = 0 0 + Iterations, force evaluations = 10000 10000 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.5154 | 1.5154 | 1.5154 | 0.0 | 86.92 +Neigh | 0.014633 | 0.014633 | 0.014633 | 0.0 | 0.84 +Comm | 0.017629 | 0.017629 | 0.017629 | 0.0 | 1.01 +Output | 0.00418 | 0.00418 | 0.00418 | 0.0 | 0.24 +Modify | 0.030156 | 0.030156 | 0.030156 | 0.0 | 1.73 +Other | | 0.1615 | | | 9.26 + +Nlocal: 800 ave 800 max 800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 318 ave 318 max 318 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7003 ave 7003 max 7003 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7003 +Ave neighs/atom = 8.75375 +Neighbor list builds = 74 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/fire/log.09Janv20.neb.fire.g++.4 b/examples/fire/log.09Janv20.neb.fire.g++.4 new file mode 100644 index 0000000000..9ceea45f8b --- /dev/null +++ b/examples/fire/log.09Janv20.neb.fire.g++.4 @@ -0,0 +1,15 @@ +LAMMPS (09 Jan 2020) +Running on 4 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959 +10 0.82975832 0.151496 0.051405637 0.82975832 0.82890942 0.44110237 0.38602248 1.6383945 0 -2213.336 0.34232243 -2212.9441 0.67673819 -2212.8949 1 -2213.2809 +20 0.1352153 0.017969594 0.028869242 0.1352153 0.71343115 0.41634032 0.41253973 1.7292177 0 -2213.3368 0.32696596 -2212.9588 0.6532446 -2212.9204 1 -2213.333 +30 0.040631856 0.0047789392 0.0035943777 0.040631856 0.77848301 0.38922096 0.38909328 1.7666107 0 -2213.3374 0.33479277 -2212.9482 0.66840762 -2212.9544 1 -2213.3373 +40 0.010021333 0.00094141903 0.0026779237 0.010021333 0.78047283 0.38807503 0.38804134 1.765797 0 -2213.3374 0.33414241 -2212.9493 0.66764466 -2212.9529 1 -2213.3374 +41 0.0085585955 0.00080485818 0.0024573847 0.0085585955 0.78063064 0.38800164 0.38797632 1.7656661 0 -2213.3374 0.33413244 -2212.9494 0.66759535 -2212.9527 1 -2213.3374 +Climbing replica = 2 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +41 0.78063064 0.31131254 0.0024573847 0.0085585955 0.78063064 0.38800164 0.38797632 1.7656661 0 -2213.3374 0.33413244 -2212.9494 0.66759535 -2212.9527 1 -2213.3374 +51 0.077404428 0.031367667 0.0011842934 0.0024342976 0.019465249 0.51014525 0.51014291 1.761094 0 -2213.3374 0.49613471 -2212.8272 0.72707246 -2213.0479 1 -2213.3374 +61 0.012232045 0.0032274471 0.00078574104 0.0014332303 0.008388584 0.51009811 0.51009738 1.7611503 0 -2213.3374 0.49457348 -2212.8273 0.74541597 -2213.0782 1 -2213.3374 +62 0.0089103916 0.0024842796 0.00072806474 0.0014932704 0.0083939608 0.51009995 0.51009934 1.7610284 0 -2213.3374 0.49503069 -2212.8273 0.74593364 -2213.079 1 -2213.3374 diff --git a/examples/fire/log.09Janv20.neb.fire.g++.8 b/examples/fire/log.09Janv20.neb.fire.g++.8 new file mode 100644 index 0000000000..a0f0f75321 --- /dev/null +++ b/examples/fire/log.09Janv20.neb.fire.g++.8 @@ -0,0 +1,14 @@ +LAMMPS (09 Jan 2020) +Running on 8 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.14285714 -2213.1848 0.28571429 -2212.8577 0.42857143 -2212.5353 0.57142857 -2212.3131 0.71428571 -2212.192 0.85714286 -2212.0797 1 -2211.7959 +10 0.83279099 0.15218551 0.051457912 0.83279099 0.51294565 0.51146911 0.45623003 1.6449446 0 -2213.336 0.14840724 -2213.2346 0.29535615 -2213.0138 0.4417452 -2212.8419 0.58719049 -2212.8245 0.73204589 -2212.9629 0.8720532 -2213.1643 1 -2213.2807 +20 0.13499135 0.025513623 0.028873652 0.13499135 0.31173673 0.49652505 0.49272333 1.751414 0 -2213.3368 0.14539729 -2213.243 0.28705892 -2213.024 0.42611693 -2212.854 0.56353342 -2212.8403 0.69946058 -2212.9846 0.83838557 -2213.203 1 -2213.333 +30 0.045307583 0.0061820354 0.0037366106 0.042519391 0.32123848 0.49279844 0.49266844 1.8063132 0 -2213.3374 0.14088843 -2213.2542 0.28088573 -2213.0379 0.41966614 -2212.859 0.55987626 -2212.8446 0.7049047 -2213.0136 0.85267772 -2213.2453 1 -2213.3373 +40 0.01020258 0.0024688055 0.0028587701 0.01020258 0.32691899 0.49208236 0.49204824 1.8050507 0 -2213.3374 0.14078995 -2213.2543 0.2808158 -2213.038 0.42032863 -2212.8585 0.56121469 -2212.8453 0.70535554 -2213.0139 0.85229608 -2213.2444 1 -2213.3373 +41 0.008663273 0.0023142496 0.0026407777 0.008633887 0.32859141 0.49188737 0.49186145 1.8049682 0 -2213.3374 0.14071905 -2213.2544 0.28075314 -2213.0381 0.42045231 -2212.8585 0.56155466 -2212.8455 0.70564189 -2213.0143 0.85237894 -2213.2445 1 -2213.3374 +Climbing replica = 5 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +41 0.32859141 0.13237876 0.0026407777 0.008633887 0.32859141 0.49188737 0.49186145 1.8049682 0 -2213.3374 0.14071905 -2213.2544 0.28075314 -2213.0381 0.42045231 -2212.8585 0.56155466 -2212.8455 0.70564189 -2213.0143 0.85237894 -2213.2445 1 -2213.3374 +51 0.040958022 0.016469867 0.0005521899 0.0016920665 0.040958022 0.50982635 0.50982533 1.8022601 0 -2213.3374 0.13880123 -2213.2577 0.26695723 -2213.0629 0.37347534 -2212.9058 0.4947259 -2212.8276 0.66038346 -2212.9436 0.8406605 -2213.2262 1 -2213.3374 +60 0.0086936374 0.0031014459 0.00019536798 0.0014152883 0.0028728935 0.51009384 0.5100937 1.8047724 0 -2213.3374 0.12947154 -2213.2696 0.25490265 -2213.0841 0.37918482 -2212.8998 0.502053 -2212.8273 0.66626732 -2212.9516 0.83109228 -2213.2129 1 -2213.3374 diff --git a/examples/fire/log.09Janv20.neb.fire_mod.g++.4 b/examples/fire/log.09Janv20.neb.fire_mod.g++.4 new file mode 100644 index 0000000000..dfd4caab24 --- /dev/null +++ b/examples/fire/log.09Janv20.neb.fire_mod.g++.4 @@ -0,0 +1,13 @@ +LAMMPS (09 Jan 2020) +Running on 4 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959 +10 0.48320283 0.070875032 0.038616783 0.48320283 0.73566671 0.43244307 0.41490356 1.6995075 0 -2213.3364 0.32902356 -2212.9569 0.65268687 -2212.904 1 -2213.3189 +20 0.04588662 0.0059014273 0.013607587 0.04588662 0.7620294 0.39621211 0.39588855 1.754979 0 -2213.3372 0.32672928 -2212.9586 0.66103382 -2212.941 1 -2213.3369 +30 0.012046386 0.0023677314 0.0024864261 0.012046386 0.77394417 0.390621 0.39059583 1.7683216 0 -2213.3374 0.33656712 -2212.9468 0.66993108 -2212.956 1 -2213.3374 +32 0.0082265111 0.002338617 0.0024204614 0.0082265111 0.77424743 0.39048139 0.39045939 1.7683165 0 -2213.3374 0.33645819 -2212.9469 0.66981988 -2212.9558 1 -2213.3374 +Climbing replica = 2 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +32 0.77424743 0.30840645 0.0024204614 0.0082265111 0.77424743 0.39048139 0.39045939 1.7683165 0 -2213.3374 0.33645819 -2212.9469 0.66981988 -2212.9558 1 -2213.3374 +42 0.10894394 0.044043242 0.0013210541 0.0029131753 0.021916453 0.5102364 0.51023223 1.7634332 0 -2213.3374 0.49598665 -2212.8272 0.71765441 -2213.0326 1 -2213.3374 +50 0.0068513242 0.0010095684 0.00065625863 0.001215472 0.0066965947 0.51011571 0.51011496 1.7619971 0 -2213.3374 0.49559669 -2212.8273 0.74807431 -2213.0827 1 -2213.3374 diff --git a/examples/fire/log.09Janv20.neb.fire_mod.g++.8 b/examples/fire/log.09Janv20.neb.fire_mod.g++.8 new file mode 100644 index 0000000000..2048909e00 --- /dev/null +++ b/examples/fire/log.09Janv20.neb.fire_mod.g++.8 @@ -0,0 +1,14 @@ +LAMMPS (09 Jan 2020) +Running on 8 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.14285714 -2213.1848 0.28571429 -2212.8577 0.42857143 -2212.5353 0.57142857 -2212.3131 0.71428571 -2212.192 0.85714286 -2212.0797 1 -2211.7959 +10 0.48475755 0.071114508 0.038599753 0.48475755 0.37640584 0.50318641 0.48560785 1.7145875 0 -2213.3364 0.1447689 -2213.2412 0.28627124 -2213.0244 0.42632938 -2212.8531 0.56539552 -2212.8332 0.7032047 -2212.9696 0.83935165 -2213.178 1 -2213.3188 +20 0.046926614 0.006867162 0.013743996 0.046926614 0.28004989 0.49743548 0.49710086 1.7876287 0 -2213.3372 0.142513 -2213.2504 0.28233628 -2213.034 0.41881659 -2212.8597 0.55388168 -2212.8398 0.69295642 -2212.9888 0.84301311 -2213.2259 1 -2213.3369 +30 0.012933981 0.0025468388 0.0021659256 0.012933981 0.33105878 0.49161235 0.49157812 1.8094495 0 -2213.3374 0.13877456 -2213.2574 0.2776974 -2213.0439 0.41817927 -2212.8603 0.5617581 -2212.8458 0.70750491 -2213.0183 0.85397925 -2213.2476 1 -2213.3374 +32 0.0094719828 0.002190111 0.0020531136 0.0094719828 0.33155635 0.49154859 0.49152008 1.8093908 0 -2213.3374 0.13875933 -2213.2574 0.2777511 -2213.0437 0.41830977 -2212.8602 0.56184682 -2212.8458 0.70752982 -2213.0184 0.8539532 -2213.2475 1 -2213.3374 +Climbing replica = 5 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +32 0.33155635 0.13350858 0.0020531136 0.0094719828 0.33155635 0.49154859 0.49152008 1.8093908 0 -2213.3374 0.13875933 -2213.2574 0.2777511 -2213.0437 0.41830977 -2212.8602 0.56184682 -2212.8458 0.70752982 -2213.0184 0.8539532 -2213.2475 1 -2213.3374 +42 0.054183917 0.021868092 0.00037963557 0.0016877522 0.054183917 0.50961909 0.50961819 1.8035718 0 -2213.3374 0.13834505 -2213.2584 0.26708756 -2213.0628 0.37311054 -2212.9062 0.49221559 -2212.8278 0.660749 -2212.9444 0.84197285 -2213.2284 1 -2213.3374 +52 0.022191714 0.0081097792 0.00012251534 0.00045278336 0.018020069 0.51004165 0.51004156 1.806295 0 -2213.3374 0.11858703 -2213.2817 0.2484601 -2213.0953 0.37835084 -2212.9009 0.49927321 -2212.8273 0.66777338 -2212.9539 0.83280212 -2213.2156 1 -2213.3374 +61 0.0083637188 0.0032627544 8.8875493e-05 0.00028087968 0.0034720486 0.51009259 0.51009255 1.8057964 0 -2213.3374 0.12337729 -2213.2765 0.24928935 -2213.0938 0.37439488 -2212.9054 0.50189879 -2212.8273 0.66754201 -2212.9535 0.83596085 -2213.22 1 -2213.3374 diff --git a/examples/fire/log.09Janv20.neb.fire_mod_old.g++.4 b/examples/fire/log.09Janv20.neb.fire_mod_old.g++.4 new file mode 100644 index 0000000000..0aeef8a531 --- /dev/null +++ b/examples/fire/log.09Janv20.neb.fire_mod_old.g++.4 @@ -0,0 +1,23 @@ +LAMMPS (09 Jan 2020) +Running on 4 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959 +10 1.3693388 0.28041646 0.070738081 1.3693388 1.0855833 0.49695052 0.30796931 1.5832462 0 -2213.3353 0.35022053 -2212.92 0.69816488 -2212.8384 1 -2213.1464 +20 1.1002508 0.21873472 0.049142357 1.1002508 0.96650653 0.44246122 0.38196494 1.6785075 0 -2213.3362 0.34083391 -2212.9409 0.66986112 -2212.8937 1 -2213.2757 +30 0.51368685 0.060842471 0.039205784 0.51368685 0.75179947 0.42112286 0.40449278 1.7009906 0 -2213.3364 0.33411939 -2212.9506 0.66142227 -2212.9153 1 -2213.3198 +40 0.35823734 0.045892314 0.033965264 0.35823734 0.73284549 0.41639462 0.4075633 1.7148522 0 -2213.3366 0.33138373 -2212.9538 0.65884796 -2212.9202 1 -2213.3278 +50 0.41165748 0.076994838 0.021380826 0.41165748 0.78427738 0.40229169 0.39779205 1.7632679 0 -2213.3371 0.32419234 -2212.9593 0.65452671 -2212.9348 1 -2213.3326 +60 0.076915443 0.010958664 0.016926588 0.076915443 0.75408409 0.39957497 0.39862604 1.7606518 0 -2213.3372 0.32519215 -2212.9591 0.65667393 -2212.9376 1 -2213.3362 +70 0.10481382 0.015447066 0.014548011 0.10481382 0.76748189 0.39515902 0.3946702 1.7555947 0 -2213.3372 0.32808712 -2212.9568 0.66188046 -2212.9421 1 -2213.3367 +80 0.080915257 0.008490983 0.012981317 0.080915257 0.76868863 0.39409972 0.39377313 1.7563219 0 -2213.3373 0.32892342 -2212.9557 0.6623966 -2212.9432 1 -2213.3369 +90 0.03261844 0.0036037258 0.010975647 0.03261844 0.77019393 0.39275317 0.39258035 1.7570762 0 -2213.3373 0.33001491 -2212.9544 0.66324116 -2212.9445 1 -2213.3371 +100 0.053370763 0.0072724044 0.009243639 0.053370763 0.77457554 0.39117385 0.391031 1.7582617 0 -2213.3373 0.33114311 -2212.9531 0.66427428 -2212.9461 1 -2213.3372 +Climbing replica = 3 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +100 0.77457554 0.30675535 0.009243639 0.053370763 0.77457554 0.39117385 0.391031 1.7582617 0 -2213.3373 0.33114311 -2212.9531 0.66427428 -2212.9461 1 -2213.3372 +110 0.25585774 0.10268695 0.0070464547 0.0681587 0.14797757 0.50920581 0.50909423 1.7558262 0 -2213.3374 0.31405087 -2212.9805 0.48492192 -2212.8281 1 -2213.3372 +120 0.11790673 0.046047759 0.0056305403 0.032412928 0.073256467 0.51011765 0.51007105 1.7564765 0 -2213.3374 0.28119336 -2213.0335 0.49788361 -2212.8272 1 -2213.3373 +130 0.070383648 0.012735737 0.0040321557 0.011560639 0.070383648 0.51017901 0.51016087 1.7586689 0 -2213.3374 0.25054735 -2213.0848 0.50803649 -2212.8272 1 -2213.3374 +140 0.031165303 0.0054585981 0.0037609991 0.0081879563 0.031165303 0.51010628 0.51009071 1.7588792 0 -2213.3374 0.2509652 -2213.084 0.50725262 -2212.8273 1 -2213.3374 +150 0.032102393 0.0051272026 0.0029882352 0.0078487546 0.032102393 0.51012806 0.51011832 1.7587138 0 -2213.3374 0.25247871 -2213.081 0.50452467 -2212.8273 1 -2213.3374 +153 0.0098882985 0.0021249062 0.0028642357 0.0047391334 0.0068711217 0.51010879 0.51009999 1.7588126 0 -2213.3374 0.25247357 -2213.0811 0.50451804 -2212.8273 1 -2213.3374 diff --git a/examples/fire/log.09Janv20.neb.fire_mod_old.g++.8 b/examples/fire/log.09Janv20.neb.fire_mod_old.g++.8 new file mode 100644 index 0000000000..86d8665e06 --- /dev/null +++ b/examples/fire/log.09Janv20.neb.fire_mod_old.g++.8 @@ -0,0 +1,25 @@ +LAMMPS (09 Jan 2020) +Running on 8 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.14285714 -2213.1848 0.28571429 -2212.8577 0.42857143 -2212.5353 0.57142857 -2212.3131 0.71428571 -2212.192 0.85714286 -2212.0797 1 -2211.7959 +10 1.3733952 0.28091862 0.070816258 1.3733952 0.8486803 0.56001239 0.3703372 1.585382 0 -2213.3353 0.1507806 -2213.2252 0.30063588 -2212.994 0.45029991 -2212.8095 0.59994263 -2212.7753 0.7496139 -2212.8912 0.89858029 -2213.0683 1 -2213.1457 +20 1.092582 0.20848565 0.049208846 1.092582 0.67749217 0.51312948 0.45351955 1.6893895 0 -2213.3362 0.14936576 -2213.2335 0.29517709 -2213.0109 0.44023761 -2212.8383 0.58433586 -2212.823 0.72824623 -2212.9685 0.86563155 -2213.1656 1 -2213.2765 +30 0.51394672 0.065440154 0.039324493 0.51394672 0.3958278 0.49724388 0.48072013 1.7159739 0 -2213.3364 0.14741033 -2213.2378 0.29093102 -2213.0178 0.43329455 -2212.8488 0.57560149 -2212.8391 0.71699492 -2212.9908 0.85518626 -2213.2019 1 -2213.3199 +40 0.3585576 0.049551349 0.034062896 0.3585576 0.35880033 0.49523368 0.48643307 1.7331908 0 -2213.3366 0.1468741 -2213.2401 0.28995894 -2213.0199 0.43116537 -2212.8509 0.57200904 -2212.8414 0.71172557 -2212.9933 0.85019682 -2213.2079 1 -2213.3278 +50 0.44071315 0.082631584 0.022058757 0.44071315 0.37223078 0.49368273 0.48892253 1.798835 0 -2213.3371 0.14570064 -2213.2457 0.28667681 -2213.0242 0.42410363 -2212.8534 0.55976055 -2212.8434 0.69487743 -2212.9955 0.83779975 -2213.2217 1 -2213.3324 +60 0.077895494 0.011715318 0.01696469 0.077895494 0.32663094 0.49291962 0.49197362 1.7955425 0 -2213.3372 0.1454209 -2213.2463 0.2868202 -2213.0251 0.42463425 -2212.854 0.56068056 -2212.8442 0.69668441 -2212.9982 0.84064029 -2213.2268 1 -2213.3362 +70 0.11340967 0.020267586 0.014639143 0.11200288 0.32902721 0.49268033 0.49216997 1.7893615 0 -2213.3372 0.14432947 -2213.2481 0.28644798 -2213.0271 0.42527709 -2212.8546 0.56239953 -2212.8445 0.70115891 -2213.0022 0.84751195 -2213.2328 1 -2213.3367 +80 0.059890228 0.0072324994 0.013525373 0.058536736 0.32663552 0.49254358 0.49222746 1.7897234 0 -2213.3372 0.14416888 -2213.2483 0.28619681 -2213.0275 0.42510701 -2212.8548 0.5624421 -2212.8447 0.70158835 -2213.0031 0.84785092 -2213.2336 1 -2213.3369 +90 0.046425179 0.0085878339 0.012661487 0.044701202 0.32705463 0.49239983 0.49214608 1.7902988 0 -2213.3373 0.14397996 -2213.2486 0.28591514 -2213.0281 0.42492825 -2212.8549 0.56254967 -2212.8449 0.70215415 -2213.0043 0.84829939 -2213.2344 1 -2213.337 +100 0.10492073 0.011902365 0.0086596336 0.098577447 0.33783582 0.49131393 0.49111204 1.7952617 0 -2213.3373 0.14284709 -2213.2507 0.28418505 -2213.0317 0.42398447 -2212.8559 0.5637284 -2212.846 0.70592525 -2213.0117 0.85128864 -2213.2397 1 -2213.3371 +Climbing replica = 5 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +100 0.33783582 0.13401694 0.0086596336 0.098577447 0.33783582 0.49131393 0.49111204 1.7952617 0 -2213.3373 0.14284709 -2213.2507 0.28418505 -2213.0317 0.42398447 -2212.8559 0.5637284 -2212.846 0.70592525 -2213.0117 0.85128864 -2213.2397 1 -2213.3371 +110 0.18587506 0.036451754 0.010634469 0.17023192 0.096871396 0.51011217 0.50966159 1.7980162 0 -2213.3374 0.14250254 -2213.2514 0.28367135 -2213.0327 0.42003349 -2212.8588 0.50682002 -2212.8272 0.70273624 -2213.0073 0.85172992 -2213.241 1 -2213.3369 +120 0.10027564 0.032272806 0.0066799491 0.069972769 0.04600783 0.51006637 0.50996326 1.7980446 0 -2213.3374 0.14245419 -2213.2516 0.28333857 -2213.0334 0.41656844 -2212.8616 0.50571617 -2212.8273 0.69946889 -2213.0023 0.85165952 -2213.2413 1 -2213.3373 +130 0.061140793 0.022612825 0.0051287229 0.035432028 0.023420936 0.51012054 0.51007667 1.79856 0 -2213.3374 0.14224093 -2213.252 0.28182793 -2213.0361 0.40850953 -2212.8685 0.50337537 -2212.8272 0.69184303 -2212.9904 0.85074583 -2213.2402 1 -2213.3373 +140 0.034227221 0.013436677 0.0033777969 0.012466833 0.012341194 0.51010526 0.5100916 1.7997532 0 -2213.3374 0.14115179 -2213.254 0.27552835 -2213.0474 0.39134491 -2212.8853 0.50005108 -2212.8273 0.67579228 -2212.9658 0.84597693 -2213.2336 1 -2213.3374 +150 0.031519482 0.012310467 0.003215866 0.0067823368 0.0094298698 0.51010745 0.51009621 1.799913 0 -2213.3374 0.1407836 -2213.2545 0.27442232 -2213.0493 0.39094764 -2212.8858 0.50040612 -2212.8273 0.67547004 -2212.9653 0.84498145 -2213.2322 1 -2213.3374 +160 0.02145751 0.006224623 0.0025005459 0.015465641 0.009264856 0.51010724 0.51009839 1.8012956 0 -2213.3374 0.13767881 -2213.2589 0.26720429 -2213.0621 0.38791572 -2212.8894 0.50222367 -2212.8273 0.67294161 -2212.9614 0.83875897 -2213.2236 1 -2213.3374 +170 0.066130312 0.0055647193 0.0038237308 0.038908839 0.020979589 0.51009997 0.51007791 1.8039701 0 -2213.3374 0.13100945 -2213.2676 0.25738978 -2213.0796 0.3821429 -2212.8962 0.50312597 -2212.8273 0.66833145 -2212.9546 0.83201742 -2213.2142 1 -2213.3374 +175 0.008829511 0.0032927835 0.00089755332 0.0014591785 0.0043357949 0.51009467 0.51009389 1.8039465 0 -2213.3374 0.13086052 -2213.2678 0.2573384 -2213.0797 0.38201967 -2212.8964 0.50305513 -2212.8273 0.66828977 -2212.9546 0.83216025 -2213.2144 1 -2213.3374 diff --git a/examples/fire/log.09Janv20.neb.fire_old.g++.4 b/examples/fire/log.09Janv20.neb.fire_old.g++.4 new file mode 100644 index 0000000000..0aeef8a531 --- /dev/null +++ b/examples/fire/log.09Janv20.neb.fire_old.g++.4 @@ -0,0 +1,23 @@ +LAMMPS (09 Jan 2020) +Running on 4 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959 +10 1.3693388 0.28041646 0.070738081 1.3693388 1.0855833 0.49695052 0.30796931 1.5832462 0 -2213.3353 0.35022053 -2212.92 0.69816488 -2212.8384 1 -2213.1464 +20 1.1002508 0.21873472 0.049142357 1.1002508 0.96650653 0.44246122 0.38196494 1.6785075 0 -2213.3362 0.34083391 -2212.9409 0.66986112 -2212.8937 1 -2213.2757 +30 0.51368685 0.060842471 0.039205784 0.51368685 0.75179947 0.42112286 0.40449278 1.7009906 0 -2213.3364 0.33411939 -2212.9506 0.66142227 -2212.9153 1 -2213.3198 +40 0.35823734 0.045892314 0.033965264 0.35823734 0.73284549 0.41639462 0.4075633 1.7148522 0 -2213.3366 0.33138373 -2212.9538 0.65884796 -2212.9202 1 -2213.3278 +50 0.41165748 0.076994838 0.021380826 0.41165748 0.78427738 0.40229169 0.39779205 1.7632679 0 -2213.3371 0.32419234 -2212.9593 0.65452671 -2212.9348 1 -2213.3326 +60 0.076915443 0.010958664 0.016926588 0.076915443 0.75408409 0.39957497 0.39862604 1.7606518 0 -2213.3372 0.32519215 -2212.9591 0.65667393 -2212.9376 1 -2213.3362 +70 0.10481382 0.015447066 0.014548011 0.10481382 0.76748189 0.39515902 0.3946702 1.7555947 0 -2213.3372 0.32808712 -2212.9568 0.66188046 -2212.9421 1 -2213.3367 +80 0.080915257 0.008490983 0.012981317 0.080915257 0.76868863 0.39409972 0.39377313 1.7563219 0 -2213.3373 0.32892342 -2212.9557 0.6623966 -2212.9432 1 -2213.3369 +90 0.03261844 0.0036037258 0.010975647 0.03261844 0.77019393 0.39275317 0.39258035 1.7570762 0 -2213.3373 0.33001491 -2212.9544 0.66324116 -2212.9445 1 -2213.3371 +100 0.053370763 0.0072724044 0.009243639 0.053370763 0.77457554 0.39117385 0.391031 1.7582617 0 -2213.3373 0.33114311 -2212.9531 0.66427428 -2212.9461 1 -2213.3372 +Climbing replica = 3 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +100 0.77457554 0.30675535 0.009243639 0.053370763 0.77457554 0.39117385 0.391031 1.7582617 0 -2213.3373 0.33114311 -2212.9531 0.66427428 -2212.9461 1 -2213.3372 +110 0.25585774 0.10268695 0.0070464547 0.0681587 0.14797757 0.50920581 0.50909423 1.7558262 0 -2213.3374 0.31405087 -2212.9805 0.48492192 -2212.8281 1 -2213.3372 +120 0.11790673 0.046047759 0.0056305403 0.032412928 0.073256467 0.51011765 0.51007105 1.7564765 0 -2213.3374 0.28119336 -2213.0335 0.49788361 -2212.8272 1 -2213.3373 +130 0.070383648 0.012735737 0.0040321557 0.011560639 0.070383648 0.51017901 0.51016087 1.7586689 0 -2213.3374 0.25054735 -2213.0848 0.50803649 -2212.8272 1 -2213.3374 +140 0.031165303 0.0054585981 0.0037609991 0.0081879563 0.031165303 0.51010628 0.51009071 1.7588792 0 -2213.3374 0.2509652 -2213.084 0.50725262 -2212.8273 1 -2213.3374 +150 0.032102393 0.0051272026 0.0029882352 0.0078487546 0.032102393 0.51012806 0.51011832 1.7587138 0 -2213.3374 0.25247871 -2213.081 0.50452467 -2212.8273 1 -2213.3374 +153 0.0098882985 0.0021249062 0.0028642357 0.0047391334 0.0068711217 0.51010879 0.51009999 1.7588126 0 -2213.3374 0.25247357 -2213.0811 0.50451804 -2212.8273 1 -2213.3374 diff --git a/examples/fire/log.09Janv20.neb.fire_old.g++.8 b/examples/fire/log.09Janv20.neb.fire_old.g++.8 new file mode 100644 index 0000000000..86d8665e06 --- /dev/null +++ b/examples/fire/log.09Janv20.neb.fire_old.g++.8 @@ -0,0 +1,25 @@ +LAMMPS (09 Jan 2020) +Running on 8 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.14285714 -2213.1848 0.28571429 -2212.8577 0.42857143 -2212.5353 0.57142857 -2212.3131 0.71428571 -2212.192 0.85714286 -2212.0797 1 -2211.7959 +10 1.3733952 0.28091862 0.070816258 1.3733952 0.8486803 0.56001239 0.3703372 1.585382 0 -2213.3353 0.1507806 -2213.2252 0.30063588 -2212.994 0.45029991 -2212.8095 0.59994263 -2212.7753 0.7496139 -2212.8912 0.89858029 -2213.0683 1 -2213.1457 +20 1.092582 0.20848565 0.049208846 1.092582 0.67749217 0.51312948 0.45351955 1.6893895 0 -2213.3362 0.14936576 -2213.2335 0.29517709 -2213.0109 0.44023761 -2212.8383 0.58433586 -2212.823 0.72824623 -2212.9685 0.86563155 -2213.1656 1 -2213.2765 +30 0.51394672 0.065440154 0.039324493 0.51394672 0.3958278 0.49724388 0.48072013 1.7159739 0 -2213.3364 0.14741033 -2213.2378 0.29093102 -2213.0178 0.43329455 -2212.8488 0.57560149 -2212.8391 0.71699492 -2212.9908 0.85518626 -2213.2019 1 -2213.3199 +40 0.3585576 0.049551349 0.034062896 0.3585576 0.35880033 0.49523368 0.48643307 1.7331908 0 -2213.3366 0.1468741 -2213.2401 0.28995894 -2213.0199 0.43116537 -2212.8509 0.57200904 -2212.8414 0.71172557 -2212.9933 0.85019682 -2213.2079 1 -2213.3278 +50 0.44071315 0.082631584 0.022058757 0.44071315 0.37223078 0.49368273 0.48892253 1.798835 0 -2213.3371 0.14570064 -2213.2457 0.28667681 -2213.0242 0.42410363 -2212.8534 0.55976055 -2212.8434 0.69487743 -2212.9955 0.83779975 -2213.2217 1 -2213.3324 +60 0.077895494 0.011715318 0.01696469 0.077895494 0.32663094 0.49291962 0.49197362 1.7955425 0 -2213.3372 0.1454209 -2213.2463 0.2868202 -2213.0251 0.42463425 -2212.854 0.56068056 -2212.8442 0.69668441 -2212.9982 0.84064029 -2213.2268 1 -2213.3362 +70 0.11340967 0.020267586 0.014639143 0.11200288 0.32902721 0.49268033 0.49216997 1.7893615 0 -2213.3372 0.14432947 -2213.2481 0.28644798 -2213.0271 0.42527709 -2212.8546 0.56239953 -2212.8445 0.70115891 -2213.0022 0.84751195 -2213.2328 1 -2213.3367 +80 0.059890228 0.0072324994 0.013525373 0.058536736 0.32663552 0.49254358 0.49222746 1.7897234 0 -2213.3372 0.14416888 -2213.2483 0.28619681 -2213.0275 0.42510701 -2212.8548 0.5624421 -2212.8447 0.70158835 -2213.0031 0.84785092 -2213.2336 1 -2213.3369 +90 0.046425179 0.0085878339 0.012661487 0.044701202 0.32705463 0.49239983 0.49214608 1.7902988 0 -2213.3373 0.14397996 -2213.2486 0.28591514 -2213.0281 0.42492825 -2212.8549 0.56254967 -2212.8449 0.70215415 -2213.0043 0.84829939 -2213.2344 1 -2213.337 +100 0.10492073 0.011902365 0.0086596336 0.098577447 0.33783582 0.49131393 0.49111204 1.7952617 0 -2213.3373 0.14284709 -2213.2507 0.28418505 -2213.0317 0.42398447 -2212.8559 0.5637284 -2212.846 0.70592525 -2213.0117 0.85128864 -2213.2397 1 -2213.3371 +Climbing replica = 5 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +100 0.33783582 0.13401694 0.0086596336 0.098577447 0.33783582 0.49131393 0.49111204 1.7952617 0 -2213.3373 0.14284709 -2213.2507 0.28418505 -2213.0317 0.42398447 -2212.8559 0.5637284 -2212.846 0.70592525 -2213.0117 0.85128864 -2213.2397 1 -2213.3371 +110 0.18587506 0.036451754 0.010634469 0.17023192 0.096871396 0.51011217 0.50966159 1.7980162 0 -2213.3374 0.14250254 -2213.2514 0.28367135 -2213.0327 0.42003349 -2212.8588 0.50682002 -2212.8272 0.70273624 -2213.0073 0.85172992 -2213.241 1 -2213.3369 +120 0.10027564 0.032272806 0.0066799491 0.069972769 0.04600783 0.51006637 0.50996326 1.7980446 0 -2213.3374 0.14245419 -2213.2516 0.28333857 -2213.0334 0.41656844 -2212.8616 0.50571617 -2212.8273 0.69946889 -2213.0023 0.85165952 -2213.2413 1 -2213.3373 +130 0.061140793 0.022612825 0.0051287229 0.035432028 0.023420936 0.51012054 0.51007667 1.79856 0 -2213.3374 0.14224093 -2213.252 0.28182793 -2213.0361 0.40850953 -2212.8685 0.50337537 -2212.8272 0.69184303 -2212.9904 0.85074583 -2213.2402 1 -2213.3373 +140 0.034227221 0.013436677 0.0033777969 0.012466833 0.012341194 0.51010526 0.5100916 1.7997532 0 -2213.3374 0.14115179 -2213.254 0.27552835 -2213.0474 0.39134491 -2212.8853 0.50005108 -2212.8273 0.67579228 -2212.9658 0.84597693 -2213.2336 1 -2213.3374 +150 0.031519482 0.012310467 0.003215866 0.0067823368 0.0094298698 0.51010745 0.51009621 1.799913 0 -2213.3374 0.1407836 -2213.2545 0.27442232 -2213.0493 0.39094764 -2212.8858 0.50040612 -2212.8273 0.67547004 -2212.9653 0.84498145 -2213.2322 1 -2213.3374 +160 0.02145751 0.006224623 0.0025005459 0.015465641 0.009264856 0.51010724 0.51009839 1.8012956 0 -2213.3374 0.13767881 -2213.2589 0.26720429 -2213.0621 0.38791572 -2212.8894 0.50222367 -2212.8273 0.67294161 -2212.9614 0.83875897 -2213.2236 1 -2213.3374 +170 0.066130312 0.0055647193 0.0038237308 0.038908839 0.020979589 0.51009997 0.51007791 1.8039701 0 -2213.3374 0.13100945 -2213.2676 0.25738978 -2213.0796 0.3821429 -2212.8962 0.50312597 -2212.8273 0.66833145 -2212.9546 0.83201742 -2213.2142 1 -2213.3374 +175 0.008829511 0.0032927835 0.00089755332 0.0014591785 0.0043357949 0.51009467 0.51009389 1.8039465 0 -2213.3374 0.13086052 -2213.2678 0.2573384 -2213.0797 0.38201967 -2212.8964 0.50305513 -2212.8273 0.66828977 -2212.9546 0.83216025 -2213.2144 1 -2213.3374 diff --git a/examples/fire/log.09Janv20.neb.qm.g++.4 b/examples/fire/log.09Janv20.neb.qm.g++.4 new file mode 100644 index 0000000000..049d72b082 --- /dev/null +++ b/examples/fire/log.09Janv20.neb.qm.g++.4 @@ -0,0 +1,18 @@ +LAMMPS (09 Jan 2020) +Running on 4 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959 +10 0.24005275 0.036502104 0.036483049 0.24005275 0.68351722 0.42916118 0.41794425 1.6989349 0 -2213.3365 0.32909183 -2212.9587 0.65386736 -2212.9073 1 -2213.3253 +20 0.07940898 0.016398055 0.024706844 0.07940898 0.71637784 0.41387872 0.41157886 1.7343662 0 -2213.3369 0.32478734 -2212.9621 0.65348766 -2212.923 1 -2213.3346 +30 0.094973707 0.0083631681 0.015145947 0.035267404 0.7535772 0.40072717 0.40024605 1.7504612 0 -2213.3372 0.32705584 -2212.9584 0.65894506 -2212.9365 1 -2213.3367 +40 0.027727472 0.0044528145 0.011618173 0.022562656 0.76133752 0.39614635 0.39591731 1.7547519 0 -2213.3373 0.32873163 -2212.9562 0.66124255 -2212.9411 1 -2213.337 +50 0.01942935 0.0030110281 0.0087135562 0.015391975 0.76952681 0.39274846 0.3926388 1.7578616 0 -2213.3373 0.33022595 -2212.9543 0.66307279 -2212.9446 1 -2213.3372 +60 0.019000226 0.0016228054 0.0053426183 0.0086165952 0.77759608 0.3893686 0.38933362 1.7610433 0 -2213.3374 0.33187548 -2212.9523 0.66497618 -2212.948 1 -2213.3373 +63 0.0097473558 0.0012728697 0.004778276 0.0076133796 0.7786505 0.38888835 0.38886103 1.7615288 0 -2213.3374 0.33212079 -2212.952 0.66525353 -2212.9485 1 -2213.3373 +Climbing replica = 3 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +63 0.7786505 0.31085887 0.004778276 0.0076133796 0.7786505 0.38888835 0.38886103 1.7615288 0 -2213.3374 0.33212079 -2212.952 0.66525353 -2212.9485 1 -2213.3373 +73 0.098492019 0.033618082 0.0027887232 0.0042741347 0.036396293 0.51024836 0.51023981 1.7607191 0 -2213.3374 0.27571995 -2213.0417 0.50430689 -2212.8271 1 -2213.3374 +83 0.032231558 0.012626629 0.0020833883 0.0031571731 0.010051365 0.51014599 0.51014135 1.7602543 0 -2213.3374 0.26039027 -2213.0673 0.5035489 -2212.8272 1 -2213.3374 +93 0.010620711 0.0034681655 0.0014722232 0.0022089665 0.0056709673 0.5101128 0.51011054 1.7601229 0 -2213.3374 0.25434046 -2213.0777 0.50383318 -2212.8273 1 -2213.3374 +94 0.0096723674 0.0031191785 0.0014334811 0.002149467 0.0054516532 0.51011153 0.51010939 1.7601211 0 -2213.3374 0.25413802 -2213.078 0.50385902 -2212.8273 1 -2213.3374 diff --git a/examples/fire/log.09Janv20.neb.qm.g++.8 b/examples/fire/log.09Janv20.neb.qm.g++.8 new file mode 100644 index 0000000000..2b28a066a4 --- /dev/null +++ b/examples/fire/log.09Janv20.neb.qm.g++.8 @@ -0,0 +1,21 @@ +LAMMPS (09 Jan 2020) +Running on 8 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.14285714 -2213.1848 0.28571429 -2212.8577 0.42857143 -2212.5353 0.57142857 -2212.3131 0.71428571 -2212.192 0.85714286 -2212.0797 1 -2211.7959 +10 0.45237221 0.062369106 0.043713415 0.45237221 0.33984237 0.50434364 0.47974444 1.681593 0 -2213.3362 0.145972 -2213.2393 0.28963267 -2213.0224 0.43234899 -2212.8512 0.57436617 -2212.8319 0.71564291 -2212.9699 0.85294239 -2213.1766 1 -2213.3116 +20 0.17466055 0.019608542 0.027733064 0.16054263 0.29142661 0.49877454 0.49547267 1.7524163 0 -2213.3369 0.14387205 -2213.2456 0.28439667 -2213.0291 0.42233932 -2212.8573 0.5588361 -2212.8381 0.69513708 -2212.9781 0.83702043 -2213.2011 1 -2213.3336 +30 0.045422642 0.010354266 0.01818213 0.045422642 0.28112975 0.49759387 0.49675173 1.7746784 0 -2213.3371 0.14290957 -2213.2488 0.28281709 -2213.0326 0.41989281 -2212.859 0.55582211 -2212.8395 0.69368801 -2212.9853 0.83973606 -2213.2161 1 -2213.3363 +40 0.038021578 0.0077863453 0.013142053 0.027303941 0.28657705 0.49667648 0.49635337 1.7848045 0 -2213.3372 0.1420496 -2213.2509 0.28169834 -2213.0351 0.41895631 -2212.8598 0.55576002 -2212.8406 0.69554601 -2212.9918 0.84293215 -2213.2247 1 -2213.3369 +50 0.023478387 0.0050438726 0.0094370881 0.017117841 0.2948129 0.4956627 0.49552819 1.7913648 0 -2213.3373 0.14130551 -2213.2524 0.28080367 -2213.0371 0.41862494 -2212.8601 0.55666336 -2212.8417 0.69796419 -2212.9977 0.84561062 -2213.2308 1 -2213.3372 +60 0.015568349 0.0036585595 0.0065356733 0.010880239 0.30476692 0.49454143 0.49448589 1.7961707 0 -2213.3374 0.14069048 -2213.2537 0.28018046 -2213.0385 0.41875119 -2212.86 0.55806463 -2212.8428 0.70047903 -2213.0032 0.84789117 -2213.2356 1 -2213.3373 +70 0.011117037 0.002930771 0.0046665969 0.0074340459 0.31343722 0.4935777 0.49355166 1.7991441 0 -2213.3374 0.14033265 -2213.2544 0.27992696 -2213.0392 0.41915513 -2212.8596 0.55940642 -2212.8438 0.70245129 -2213.0073 0.8494878 -2213.2387 1 -2213.3373 +77 0.0095031741 0.0025470028 0.0037787977 0.0059130847 0.31843202 0.4930196 0.49300314 1.8005357 0 -2213.3374 0.14019726 -2213.2547 0.27989276 -2213.0394 0.41949004 -2212.8594 0.56021118 -2212.8444 0.7035183 -2213.0094 0.85030235 -2213.2402 1 -2213.3374 +Climbing replica = 5 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +77 0.31843202 0.12858086 0.0037787977 0.0059130847 0.31843202 0.4930196 0.49300314 1.8005357 0 -2213.3374 0.14019726 -2213.2547 0.27989276 -2213.0394 0.41949004 -2212.8594 0.56021118 -2212.8444 0.7035183 -2213.0094 0.85030235 -2213.2402 1 -2213.3374 +87 0.068485358 0.020416571 0.0025906821 0.0039654836 0.024981085 0.51001438 0.51000702 1.8017658 0 -2213.3374 0.13988537 -2213.2554 0.2781578 -2213.0427 0.40602784 -2212.8709 0.50551349 -2212.8274 0.69111931 -2212.99 0.8499171 -2213.2398 1 -2213.3374 +97 0.031476072 0.0123593 0.0020332076 0.0030835531 0.0070061038 0.51009654 0.51009211 1.8020357 0 -2213.3374 0.13898543 -2213.2569 0.27381812 -2213.0504 0.39685543 -2212.8798 0.50256086 -2212.8273 0.68246582 -2212.9764 0.84621512 -2213.2346 1 -2213.3374 +107 0.028460125 0.0067640875 0.0014194664 0.0021303377 0.0026454458 0.51009858 0.51009648 1.8028 0 -2213.3374 0.13646 -2213.2604 0.26764336 -2213.0614 0.38930317 -2212.8879 0.50193579 -2212.8273 0.67546861 -2212.9656 0.8411568 -2213.2275 1 -2213.3374 +117 0.014824889 0.0055517464 0.0010985753 0.0016392459 0.0019892141 0.51009713 0.51009589 1.8033322 0 -2213.3374 0.13447899 -2213.263 0.26412103 -2213.0676 0.38617147 -2212.8914 0.5020058 -2212.8273 0.67278941 -2212.9615 0.83870093 -2213.224 1 -2213.3374 +127 0.011626205 0.00404434 0.00078110388 0.0011582058 0.0014475679 0.51009594 0.51009533 1.8039369 0 -2213.3374 0.13219331 -2213.266 0.26054642 -2213.074 0.38339139 -2212.8946 0.50214085 -2212.8273 0.67071709 -2212.9584 0.83665693 -2213.2211 1 -2213.3374 +132 0.0089531814 0.0035807918 0.00069218572 0.0010244011 0.0012955882 0.51009566 0.51009518 1.8041186 0 -2213.3374 0.13150535 -2213.2669 0.2595308 -2213.0758 0.38264847 -2212.8955 0.50218195 -2212.8273 0.67024326 -2212.9576 0.83617539 -2213.2204 1 -2213.3374 diff --git a/src/min.cpp b/src/min.cpp index 003fd18b81..f8ed11375c 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -58,6 +58,18 @@ Min::Min(LAMMPS *lmp) : Pointers(lmp) linestyle = 1; normstyle = TWO; + delaystep = 20; + dtgrow = 1.1; + dtshrink = 0.5; + alpha0 = 0.25; + alphashrink = 0.99; + tmax = 10.0; + tmin = 0.02; + integrator = 0; + halfstepback_flag = 1; + delaystep_start_flag = 1; + max_vdotf_negatif = 2000; + elist_global = elist_atom = NULL; vlist_global = vlist_atom = cvlist_atom = NULL; @@ -184,6 +196,10 @@ void Min::init() neighbor->dist_check = 1; niter = neval = 0; + + // store timestep size (important for variable timestep minimizer) + + dtinit = update->dt; } /* ---------------------------------------------------------------------- @@ -473,6 +489,10 @@ void Min::cleanup() modify->delete_fix("MINIMIZE"); domain->box_too_small_check(); + + // reset timestep size (important for variable timestep minimizer) + + update->dt = dtinit; } /* ---------------------------------------------------------------------- @@ -658,6 +678,58 @@ void Min::modify_params(int narg, char **arg) if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command"); dmax = force->numeric(FLERR,arg[iarg+1]); iarg += 2; + } else if (strcmp(arg[iarg],"delaystep") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command"); + delaystep = force->numeric(FLERR,arg[iarg+1]); + iarg += 2; + } else if (strcmp(arg[iarg],"dtgrow") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command"); + dtgrow = force->numeric(FLERR,arg[iarg+1]); + iarg += 2; + } else if (strcmp(arg[iarg],"dtshrink") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command"); + dtshrink = force->numeric(FLERR,arg[iarg+1]); + iarg += 2; + } else if (strcmp(arg[iarg],"alpha0") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command"); + alpha0 = force->numeric(FLERR,arg[iarg+1]); + iarg += 2; + } else if (strcmp(arg[iarg],"alphashrink") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command"); + alphashrink = force->numeric(FLERR,arg[iarg+1]); + iarg += 2; + } else if (strcmp(arg[iarg],"tmax") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command"); + tmax = force->numeric(FLERR,arg[iarg+1]); + iarg += 2; + } else if (strcmp(arg[iarg],"tmin") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command"); + tmin = force->numeric(FLERR,arg[iarg+1]); + iarg += 2; + } else if (strcmp(arg[iarg],"halfstepback") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command"); + if (strcmp(arg[iarg+1],"yes") == 0) halfstepback_flag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) halfstepback_flag = 0; + else error->all(FLERR,"Illegal min_modify command"); + iarg += 2; + } else if (strcmp(arg[iarg],"initialdelay") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command"); + if (strcmp(arg[iarg+1],"yes") == 0) delaystep_start_flag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) delaystep_start_flag = 0; + else error->all(FLERR,"Illegal min_modify command"); + iarg += 2; + } else if (strcmp(arg[iarg],"vdfmax") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command"); + max_vdotf_negatif = force->numeric(FLERR,arg[iarg+1]); + iarg += 2; + } else if (strcmp(arg[iarg],"integrator") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command"); + if (strcmp(arg[iarg+1],"eulerimplicit") == 0) integrator = 0; + else if (strcmp(arg[iarg+1],"verlet") == 0) integrator = 1; + else if (strcmp(arg[iarg+1],"leapfrog") == 0) integrator = 2; + else if (strcmp(arg[iarg+1],"eulerexplicit") == 0) integrator = 3; + else error->all(FLERR,"Illegal min_modify command"); + iarg += 2; } else if (strcmp(arg[iarg],"line") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command"); if (strcmp(arg[iarg+1],"backtrack") == 0) linestyle = 0; @@ -999,6 +1071,7 @@ char *Min::stopstrings(int n) "quadratic factors are zero", "trust region too small", "HFTN minimizer error", - "walltime limit reached"}; + "walltime limit reached", + "max iterations with v.f negative"}; return (char *) strings[n]; } diff --git a/src/min.h b/src/min.h index ba47f95410..b23c9b6670 100644 --- a/src/min.h +++ b/src/min.h @@ -57,7 +57,7 @@ class Min : protected Pointers { // possible return values of iterate() method enum{MAXITER,MAXEVAL,ETOL,FTOL,DOWNHILL,ZEROALPHA,ZEROFORCE, - ZEROQUAD,TRSMALL,INTERROR,TIMEOUT}; + ZEROQUAD,TRSMALL,INTERROR,TIMEOUT,MAXVDOTF}; protected: int eflag,vflag; // flags for energy/virial computation @@ -70,6 +70,18 @@ class Min : protected Pointers { int normstyle; // TWO, MAX or INF flag for force norm evaluation + double dtinit; // store the default timestep + + // only for minimize style fire2 + int delaystep; // minium steps of dynamics + double dtgrow,dtshrink; // timestep increase, decrease + double alpha0,alphashrink; // mixing velocities+forces coefficient + double tmax,tmin; // timestep multiplicators max, min + int integrator; // Newton integration: euler, leapfrog, verlet... + int halfstepback_flag; // half step backward when v.f <= 0.0 + int delaystep_start_flag; // delay the initial dt_shrink + int max_vdotf_negatif; // maximum iteration with v.f > 0.0 + int nelist_global,nelist_atom; // # of PE,virial computes to check int nvlist_global,nvlist_atom,ncvlist_atom; class Compute **elist_global; // lists of PE,virial Computes diff --git a/src/min_fire.cpp b/src/min_fire.cpp index ca37e410b8..4aeeddf6b2 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -11,16 +11,26 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "min_fire.h" -#include +/* ---------------------------------------------------------------------- + Contributing authors: Julien Guénolé, CNRS and + Erik Bitzek, FAU Erlangen-Nuernberg +------------------------------------------------------------------------- */ + #include +#include "min_fire.h" #include "universe.h" #include "atom.h" -#include "error.h" #include "force.h" #include "update.h" #include "output.h" #include "timer.h" +#include "error.h" +#include "variable.h" +#include "modify.h" +#include "compute.h" +#include "domain.h" +#include "neighbor.h" +#include "comm.h" using namespace LAMMPS_NS; @@ -28,13 +38,6 @@ using namespace LAMMPS_NS; #define EPS_ENERGY 1.0e-8 -#define DELAYSTEP 5 -#define DT_GROW 1.1 -#define DT_SHRINK 0.5 -#define ALPHA0 0.1 -#define ALPHA_SHRINK 0.99 -#define TMAX 10.0 - /* ---------------------------------------------------------------------- */ MinFire::MinFire(LAMMPS *lmp) : Min(lmp) {} @@ -45,10 +48,18 @@ void MinFire::init() { Min::init(); + // simple parameters validation + + if (tmax < tmin) error->all(FLERR,"tmax has to be larger than tmin"); + if (dtgrow < 1.0) error->all(FLERR,"dtgrow has to be larger than 1.0"); + if (dtshrink > 1.0) error->all(FLERR,"dtshrink has to be smaller than 1.0"); + dt = update->dt; - dtmax = TMAX * dt; - alpha = ALPHA0; - last_negative = update->ntimestep; + dtmax = tmax * dt; + dtmin = tmin * dt; + alpha = alpha0; + last_negative = ntimestep_start = update->ntimestep; + vdotf_negatif = 0; } /* ---------------------------------------------------------------------- */ @@ -58,6 +69,22 @@ void MinFire::setup_style() double **v = atom->v; int nlocal = atom->nlocal; + // print the parameters used within fire into the log + + const char *s1[] = {"eulerimplicit","verlet","leapfrog","eulerexplicit"}; + const char *s2[] = {"no","yes"}; + + if (comm->me == 0 && logfile) { + fprintf(logfile," Parameters for fire: \n" + " dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin " + " integrator halfstepback \n" + " %4g %9i %6g %8g %6g %11g %4g %4g %13s %12s \n", + dmax, delaystep, dtgrow, dtshrink, alpha0, alphashrink, tmax, tmin, + s1[integrator], s2[halfstepback_flag]); + } + + // initialize the velocities + for (int i = 0; i < nlocal; i++) v[i][0] = v[i][1] = v[i][2] = 0.0; } @@ -88,6 +115,39 @@ int MinFire::iterate(int maxiter) alpha_final = 0.0; + // Leap Frog integration initialization + + if (integrator == 2) { + + double **f = atom->f; + double **v = atom->v; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int nlocal = atom->nlocal; + + energy_force(0); + neval++; + + dtf = -0.5 * dt * force->ftm2v; + + if (rmass) { + for (int i = 0; i < nlocal; i++) { + dtfm = dtf / rmass[i]; + v[i][0] = dtfm * f[i][0]; + v[i][1] = dtfm * f[i][1]; + v[i][2] = dtfm * f[i][2]; + } + } else { + for (int i = 0; i < nlocal; i++) { + dtfm = dtf / mass[type[i]]; + v[i][0] = dtfm * f[i][0]; + v[i][1] = dtfm * f[i][1]; + v[i][2] = dtfm * f[i][2]; + } + } + } + for (int iter = 0; iter < maxiter; iter++) { if (timer->check_timeout(niter)) @@ -96,11 +156,17 @@ int MinFire::iterate(int maxiter) ntimestep = ++update->ntimestep; niter++; - // vdotfall = v dot f + // pointers + int nlocal = atom->nlocal; double **v = atom->v; double **f = atom->f; - int nlocal = atom->nlocal; + double **x = atom->x; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + + // vdotfall = v dot f vdotf = 0.0; for (int i = 0; i < nlocal; i++) @@ -118,11 +184,14 @@ int MinFire::iterate(int maxiter) // if (v dot f) > 0: // v = (1-alpha) v + alpha |v| Fhat // |v| = length of v, Fhat = unit f - // if more than DELAYSTEP since v dot f was negative: - // increase timestep and decrease alpha + // Only: (1-alpha) and alpha |v| Fhat is calculated here + // the modificatin of v is made wihtin the integration, after v update + // if more than delaystep since v dot f was negative: + // increase timestep, update global timestep and decrease alpha if (vdotfall > 0.0) { vdotv = 0.0; + vdotf_negatif = 0; for (int i = 0; i < nlocal; i++) vdotv += v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]; MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,world); @@ -149,36 +218,59 @@ int MinFire::iterate(int maxiter) } scale1 = 1.0 - alpha; - if (fdotfall == 0.0) scale2 = 0.0; + if (fdotfall <= 1e-20) scale2 = 0.0; else scale2 = alpha * sqrt(vdotvall/fdotfall); - for (int i = 0; i < nlocal; i++) { - v[i][0] = scale1*v[i][0] + scale2*f[i][0]; - v[i][1] = scale1*v[i][1] + scale2*f[i][1]; - v[i][2] = scale1*v[i][2] + scale2*f[i][2]; + + if (ntimestep - last_negative > delaystep) { + dt = MIN(dt*dtgrow,dtmax); + update->dt = dt; + alpha *= alphashrink; } - if (ntimestep - last_negative > DELAYSTEP) { - dt = MIN(dt*DT_GROW,dtmax); - alpha *= ALPHA_SHRINK; - } - - // else (v dot f) <= 0: - // decrease timestep, reset alpha, set v = 0 + // else (v dot f) <= 0 + // if more than delaystep since starting the relaxation: + // reset alpha + // if dt*dtshrink > dtmin: + // decrease timestep + // update global timestep (for thermo output) + // half step back within the dynamics: x(t) = x(t-0.5*dt) + // reset velocities: v = 0 } else { last_negative = ntimestep; - dt *= DT_SHRINK; - alpha = ALPHA0; + int delayflag = 1; + if (ntimestep - ntimestep_start < delaystep && delaystep_start_flag) + delayflag = 0; + if (delayflag) { + alpha = alpha0; + if (dt*dtshrink >= dtmin) { + dt *= dtshrink; + update->dt = dt; + } + } + + // stopping criterion while stuck in a local bassin of the PES + + vdotf_negatif++; + if (max_vdotf_negatif > 0 && vdotf_negatif > max_vdotf_negatif) + return MAXVDOTF; + + // inertia correction + + if (halfstepback_flag) { + for (int i = 0; i < nlocal; i++) { + x[i][0] -= 0.5 * dtv * v[i][0]; + x[i][1] -= 0.5 * dtv * v[i][1]; + x[i][2] -= 0.5 * dtv * v[i][2]; + } + } + for (int i = 0; i < nlocal; i++) v[i][0] = v[i][1] = v[i][2] = 0.0; } // limit timestep so no particle moves further than dmax - double *rmass = atom->rmass; - double *mass = atom->mass; - int *type = atom->type; - dtvone = dt; for (int i = 0; i < nlocal; i++) { @@ -186,6 +278,7 @@ int MinFire::iterate(int maxiter) vmax = MAX(vmax,fabs(v[i][2])); if (dtvone*vmax > dmax) dtvone = dmax/vmax; } + MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world); // min dtv over replicas, if necessary @@ -196,43 +289,161 @@ int MinFire::iterate(int maxiter) MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld); } - dtf = dtv * force->ftm2v; + // Dynamic integration scheme: + // 0: semi-implicit Euler + // 1: velocity Verlet + // 2: leapfrog (initial half step before the iteration loop) + // 3: explicit Euler - // Euler integration step + // Semi-implicit Euler OR Leap Frog integration - double **x = atom->x; + if (integrator == 0 || integrator == 2) { - if (rmass) { - for (int i = 0; i < nlocal; i++) { - dtfm = dtf / rmass[i]; - x[i][0] += dtv * v[i][0]; - x[i][1] += dtv * v[i][1]; - x[i][2] += dtv * v[i][2]; - v[i][0] += dtfm * f[i][0]; - v[i][1] += dtfm * f[i][1]; - v[i][2] += dtfm * f[i][2]; + dtf = dtv * force->ftm2v; + + if (rmass) { + for (int i = 0; i < nlocal; i++) { + dtfm = dtf / rmass[i]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + if (vdotfall > 0.0) { + v[i][0] = scale1*v[i][0] + scale2*f[i][0]; + v[i][1] = scale1*v[i][1] + scale2*f[i][1]; + v[i][2] = scale1*v[i][2] + scale2*f[i][2]; + } + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + } else { + for (int i = 0; i < nlocal; i++) { + dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + if (vdotfall > 0.0) { + v[i][0] = scale1*v[i][0] + scale2*f[i][0]; + v[i][1] = scale1*v[i][1] + scale2*f[i][1]; + v[i][2] = scale1*v[i][2] + scale2*f[i][2]; + } + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } } - } else { - for (int i = 0; i < nlocal; i++) { - dtfm = dtf / mass[type[i]]; - x[i][0] += dtv * v[i][0]; - x[i][1] += dtv * v[i][1]; - x[i][2] += dtv * v[i][2]; - v[i][0] += dtfm * f[i][0]; - v[i][1] += dtfm * f[i][1]; - v[i][2] += dtfm * f[i][2]; + + eprevious = ecurrent; + ecurrent = energy_force(0); + neval++; + + // Velocity Verlet integration + + } else if (integrator == 1) { + + dtf = 0.5 * dtv * force->ftm2v; + + if (rmass) { + for (int i = 0; i < nlocal; i++) { + dtfm = dtf / rmass[i]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + if (vdotfall > 0.0) { + v[i][0] = scale1*v[i][0] + scale2*f[i][0]; + v[i][1] = scale1*v[i][1] + scale2*f[i][1]; + v[i][2] = scale1*v[i][2] + scale2*f[i][2]; + } + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + } else { + for (int i = 0; i < nlocal; i++) { + dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + if (vdotfall > 0.0) { + v[i][0] = scale1*v[i][0] + scale2*f[i][0]; + v[i][1] = scale1*v[i][1] + scale2*f[i][1]; + v[i][2] = scale1*v[i][2] + scale2*f[i][2]; + } + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } } + + eprevious = ecurrent; + ecurrent = energy_force(0); + neval++; + + if (rmass) { + for (int i = 0; i < nlocal; i++) { + dtfm = dtf / rmass[i]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + } else { + for (int i = 0; i < nlocal; i++) { + dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + } + + // Standard Euler integration + + } else if (integrator == 3) { + + dtf = dtv * force->ftm2v; + + if (rmass) { + for (int i = 0; i < nlocal; i++) { + dtfm = dtf / rmass[i]; + if (vdotfall > 0.0) { + v[i][0] = scale1*v[i][0] + scale2*f[i][0]; + v[i][1] = scale1*v[i][1] + scale2*f[i][1]; + v[i][2] = scale1*v[i][2] + scale2*f[i][2]; + } + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + } else { + for (int i = 0; i < nlocal; i++) { + dtfm = dtf / mass[type[i]]; + if (vdotfall > 0.0) { + v[i][0] = scale1*v[i][0] + scale2*f[i][0]; + v[i][1] = scale1*v[i][1] + scale2*f[i][1]; + v[i][2] = scale1*v[i][2] + scale2*f[i][2]; + } + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + } + + eprevious = ecurrent; + ecurrent = energy_force(0); + neval++; } - eprevious = ecurrent; - ecurrent = energy_force(0); - neval++; - // energy tolerance criterion - // only check after DELAYSTEP elapsed since velocties reset to 0 + // only check after delaystep elapsed since velocties reset to 0 // sync across replicas if running multi-replica minimization + // reset the timestep to the initial value - if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) { + if (update->etol > 0.0 && ntimestep-last_negative > delaystep) { if (update->multireplica == 0) { if (fabs(ecurrent-eprevious) < update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY)) @@ -243,12 +454,14 @@ int MinFire::iterate(int maxiter) flag = 0; else flag = 1; MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld); - if (flagall == 0) return ETOL; + if (flagall == 0) + return ETOL; } } // force tolerance criterion // sync across replicas if running multi-replica minimization + // reset the timestep to the initial value fdotf = 0.0; if (update->ftol > 0.0) { diff --git a/src/min_fire.h b/src/min_fire.h index 3cb375163e..0c4be968dc 100644 --- a/src/min_fire.h +++ b/src/min_fire.h @@ -34,9 +34,10 @@ class MinFire : public Min { int iterate(int); private: - double dt,dtmax; + double dt,dtmax,dtmin; double alpha; - bigint last_negative; + bigint last_negative,ntimestep_start; + int vdotf_negatif; }; } diff --git a/src/min_fire_old.cpp b/src/min_fire_old.cpp new file mode 100644 index 0000000000..bd76b2d1fc --- /dev/null +++ b/src/min_fire_old.cpp @@ -0,0 +1,279 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "min_fire_old.h" +#include +#include +#include "universe.h" +#include "atom.h" +#include "error.h" +#include "force.h" +#include "update.h" +#include "output.h" +#include "timer.h" + +using namespace LAMMPS_NS; + +// EPS_ENERGY = minimum normalization for energy tolerance + +#define EPS_ENERGY 1.0e-8 + +#define DELAYSTEP 5 +#define DT_GROW 1.1 +#define DT_SHRINK 0.5 +#define ALPHA0 0.1 +#define ALPHA_SHRINK 0.99 +#define TMAX 10.0 + +/* ---------------------------------------------------------------------- */ + +MinFireOld::MinFireOld(LAMMPS *lmp) : Min(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void MinFireOld::init() +{ + Min::init(); + + dt = update->dt; + dtmax = TMAX * dt; + alpha = ALPHA0; + last_negative = update->ntimestep; +} + +/* ---------------------------------------------------------------------- */ + +void MinFireOld::setup_style() +{ + double **v = atom->v; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) + v[i][0] = v[i][1] = v[i][2] = 0.0; +} + +/* ---------------------------------------------------------------------- + set current vector lengths and pointers + called after atoms have migrated +------------------------------------------------------------------------- */ + +void MinFireOld::reset_vectors() +{ + // atomic dof + + nvec = 3 * atom->nlocal; + if (nvec) xvec = atom->x[0]; + if (nvec) fvec = atom->f[0]; +} + +/* ---------------------------------------------------------------------- */ + +int MinFireOld::iterate(int maxiter) +{ + bigint ntimestep; + double vmax,vdotf,vdotfall,vdotv,vdotvall,fdotf,fdotfall; + double scale1,scale2; + double dtvone,dtv,dtf,dtfm; + int flag,flagall; + + alpha_final = 0.0; + + for (int iter = 0; iter < maxiter; iter++) { + + if (timer->check_timeout(niter)) + return TIMEOUT; + + ntimestep = ++update->ntimestep; + niter++; + + // vdotfall = v dot f + + double **v = atom->v; + double **f = atom->f; + int nlocal = atom->nlocal; + + vdotf = 0.0; + for (int i = 0; i < nlocal; i++) + vdotf += v[i][0]*f[i][0] + v[i][1]*f[i][1] + v[i][2]*f[i][2]; + MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,world); + + // sum vdotf over replicas, if necessary + // this communicator would be invalid for multiprocess replicas + + if (update->multireplica == 1) { + vdotf = vdotfall; + MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld); + } + + // if (v dot f) > 0: + // v = (1-alpha) v + alpha |v| Fhat + // |v| = length of v, Fhat = unit f + // if more than DELAYSTEP since v dot f was negative: + // increase timestep and decrease alpha + + if (vdotfall > 0.0) { + vdotv = 0.0; + for (int i = 0; i < nlocal; i++) + vdotv += v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]; + MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,world); + + // sum vdotv over replicas, if necessary + // this communicator would be invalid for multiprocess replicas + + if (update->multireplica == 1) { + vdotv = vdotvall; + MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,universe->uworld); + } + + fdotf = 0.0; + for (int i = 0; i < nlocal; i++) + fdotf += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2]; + MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,world); + + // sum fdotf over replicas, if necessary + // this communicator would be invalid for multiprocess replicas + + if (update->multireplica == 1) { + fdotf = fdotfall; + MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld); + } + + scale1 = 1.0 - alpha; + if (fdotfall == 0.0) scale2 = 0.0; + else scale2 = alpha * sqrt(vdotvall/fdotfall); + for (int i = 0; i < nlocal; i++) { + v[i][0] = scale1*v[i][0] + scale2*f[i][0]; + v[i][1] = scale1*v[i][1] + scale2*f[i][1]; + v[i][2] = scale1*v[i][2] + scale2*f[i][2]; + } + + if (ntimestep - last_negative > DELAYSTEP) { + dt = MIN(dt*DT_GROW,dtmax); + alpha *= ALPHA_SHRINK; + } + + // else (v dot f) <= 0: + // decrease timestep, reset alpha, set v = 0 + + } else { + last_negative = ntimestep; + dt *= DT_SHRINK; + alpha = ALPHA0; + for (int i = 0; i < nlocal; i++) + v[i][0] = v[i][1] = v[i][2] = 0.0; + } + + // limit timestep so no particle moves further than dmax + + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + + dtvone = dt; + + for (int i = 0; i < nlocal; i++) { + vmax = MAX(fabs(v[i][0]),fabs(v[i][1])); + vmax = MAX(vmax,fabs(v[i][2])); + if (dtvone*vmax > dmax) dtvone = dmax/vmax; + } + MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world); + + // min dtv over replicas, if necessary + // this communicator would be invalid for multiprocess replicas + + if (update->multireplica == 1) { + dtvone = dtv; + MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld); + } + + dtf = dtv * force->ftm2v; + + // Euler integration step + + double **x = atom->x; + + if (rmass) { + for (int i = 0; i < nlocal; i++) { + dtfm = dtf / rmass[i]; + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + } else { + for (int i = 0; i < nlocal; i++) { + dtfm = dtf / mass[type[i]]; + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + } + + eprevious = ecurrent; + ecurrent = energy_force(0); + neval++; + + // energy tolerance criterion + // only check after DELAYSTEP elapsed since velocties reset to 0 + // sync across replicas if running multi-replica minimization + + if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) { + if (update->multireplica == 0) { + if (fabs(ecurrent-eprevious) < + update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY)) + return ETOL; + } else { + if (fabs(ecurrent-eprevious) < + update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY)) + flag = 0; + else flag = 1; + MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld); + if (flagall == 0) return ETOL; + } + } + + // force tolerance criterion + // sync across replicas if running multi-replica minimization + + fdotf = 0.0; + if (update->ftol > 0.0) { + if (normstyle == MAX) fdotf = fnorm_max(); // max force norm + else if (normstyle == INF) fdotf = fnorm_inf(); // inf force norm + else if (normstyle == TWO) fdotf = fnorm_sqr(); // Euclidean force 2-norm + else error->all(FLERR,"Illegal min_modify command"); + if (update->multireplica == 0) { + if (fdotf < update->ftol*update->ftol) return FTOL; + } else { + if (fdotf < update->ftol*update->ftol) flag = 0; + else flag = 1; + MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld); + if (flagall == 0) return FTOL; + } + } + + // output for thermo, dump, restart files + + if (output->next == ntimestep) { + timer->stamp(); + output->write(ntimestep); + timer->stamp(Timer::OUTPUT); + } + } + + return MAXITER; +} diff --git a/src/min_fire_old.h b/src/min_fire_old.h new file mode 100644 index 0000000000..5d7afaa627 --- /dev/null +++ b/src/min_fire_old.h @@ -0,0 +1,45 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef MINIMIZE_CLASS + +MinimizeStyle(fire/old,MinFireOld) + +#else + +#ifndef LMP_MIN_FIRE_OLD_H +#define LMP_MIN_FIRE_OLD_H + +#include "min.h" + +namespace LAMMPS_NS { + +class MinFireOld : public Min { + public: + MinFireOld(class LAMMPS *); + ~MinFireOld() {} + void init(); + void setup_style(); + void reset_vectors(); + int iterate(int); + + private: + double dt,dtmax; + double alpha; + bigint last_negative; +}; + +} + +#endif +#endif