From 855b6000efcb0e8d29dc2ba3ec6f719b98c81e4a Mon Sep 17 00:00:00 2001 From: David Nicholson Date: Thu, 28 Sep 2017 16:34:18 -0400 Subject: [PATCH 01/21] initial commit. doc is in the works --- doc/src/Section_commands.txt | 4 + doc/src/Section_packages.txt | 28 + doc/src/compute_temp_uef.txt | 52 + doc/src/fix_nh_uef.txt | 715 ++++++++++++ examples/USER/uef/README | 19 + examples/USER/uef/npt_biaxial/data.wca | 1022 +++++++++++++++++ examples/USER/uef/npt_biaxial/in.npt_biaxial | 31 + .../npt_biaxial/log.30Jul16.npt_biaxial.g++.1 | 276 +++++ .../npt_biaxial/log.30Jul16.npt_biaxial.g++.4 | 276 +++++ examples/USER/uef/nvt_uniaxial/data.wca | 1022 +++++++++++++++++ .../USER/uef/nvt_uniaxial/in.nvt_uniaxial | 28 + .../log.30Jul16.npt_uniaxial.g++.1 | 273 +++++ .../log.30Jul16.npt_uniaxial.g++.4 | 273 +++++ src/Makefile | 2 +- src/USER-UEF/compute_pressure_uef.cpp | 198 ++++ src/USER-UEF/compute_pressure_uef.h | 66 ++ src/USER-UEF/compute_temp_uef.cpp | 110 ++ src/USER-UEF/compute_temp_uef.h | 60 + src/USER-UEF/dump_cfg_uef.cpp | 113 ++ src/USER-UEF/dump_cfg_uef.h | 51 + src/USER-UEF/fix_nh_uef.cpp | 846 ++++++++++++++ src/USER-UEF/fix_nh_uef.h | 125 ++ src/USER-UEF/fix_npt_uef.cpp | 33 + src/USER-UEF/fix_npt_uef.h | 50 + src/USER-UEF/fix_nvt_uef.cpp | 35 + src/USER-UEF/fix_nvt_uef.h | 50 + src/USER-UEF/uef_utils.cpp | 365 ++++++ src/USER-UEF/uef_utils.h | 139 +++ 28 files changed, 6261 insertions(+), 1 deletion(-) create mode 100644 doc/src/compute_temp_uef.txt create mode 100644 doc/src/fix_nh_uef.txt create mode 100644 examples/USER/uef/README create mode 100644 examples/USER/uef/npt_biaxial/data.wca create mode 100644 examples/USER/uef/npt_biaxial/in.npt_biaxial create mode 100644 examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.1 create mode 100644 examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.4 create mode 100644 examples/USER/uef/nvt_uniaxial/data.wca create mode 100644 examples/USER/uef/nvt_uniaxial/in.nvt_uniaxial create mode 100644 examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.1 create mode 100644 examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.4 create mode 100644 src/USER-UEF/compute_pressure_uef.cpp create mode 100644 src/USER-UEF/compute_pressure_uef.h create mode 100644 src/USER-UEF/compute_temp_uef.cpp create mode 100644 src/USER-UEF/compute_temp_uef.h create mode 100644 src/USER-UEF/dump_cfg_uef.cpp create mode 100644 src/USER-UEF/dump_cfg_uef.h create mode 100644 src/USER-UEF/fix_nh_uef.cpp create mode 100644 src/USER-UEF/fix_nh_uef.h create mode 100644 src/USER-UEF/fix_npt_uef.cpp create mode 100644 src/USER-UEF/fix_npt_uef.h create mode 100644 src/USER-UEF/fix_nvt_uef.cpp create mode 100644 src/USER-UEF/fix_nvt_uef.h create mode 100644 src/USER-UEF/uef_utils.cpp create mode 100644 src/USER-UEF/uef_utils.h diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 0d46a01424..3ac9c05e5c 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -715,8 +715,10 @@ package"_Section_start.html#start_3. "nve/manifold/rattle"_fix_nve_manifold_rattle.html, "nvk"_fix_nvk.html, "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, +"nvt/uef"_fix_nh_uef.html, "nph/eff"_fix_nh_eff.html, "npt/eff"_fix_nh_eff.html, +"npt/uef"_fix_nh_uef.html, "nve/eff"_fix_nve_eff.html, "nvt/eff"_fix_nh_eff.html, "nvt/sllod/eff"_fix_nvt_sllod_eff.html, @@ -856,6 +858,7 @@ package"_Section_start.html#start_3. "meso/t/atom"_compute_meso_t_atom.html, "pe/tally"_compute_tally.html, "pe/mol/tally"_compute_tally.html, +"pressure/uef"_compute_pressure_uef.html, "saed"_compute_saed.html, "smd/contact/radius"_compute_smd_contact_radius.html, "smd/damage"_compute_smd_damage.html, @@ -884,6 +887,7 @@ package"_Section_start.html#start_3. "temp/deform/eff"_compute_temp_deform_eff.html, "temp/region/eff"_compute_temp_region_eff.html, "temp/rotate"_compute_temp_rotate.html, +"temp/uef"_compute_temp_uef.html, "xrd"_compute_xrd.html :tb(c=6,ea=c) :line diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index d9a9fb4163..45cdd8ff48 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -150,6 +150,7 @@ Package, Description, Doc page, Example, Library "USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, - "USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, - "USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, - +"USER-UEF"_#USER-UEF, NEMD under extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, - "USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l) :line @@ -2770,6 +2771,33 @@ examples/USER/tally :ul :line +UEF package :link(UEF),h4 + +[Contents:] + +A fix style for the integration of the equations of motion under +extensional flow with proper boundary conditions, as well +as several supporting compute styles and an output option. + +[Install or un-install:] + +make yes-user-uef +make machine :pre + +make no-user-uef +make machine :pre + +[Supporting info:] + +src/USER-UEF: filenames -> commands +"fix nvt/uef"_fix_nh_uef.html +"compute pressure/uef"_compute_pressure_uef.html +"compute temp/uef"_compute_temp_uef.html +"dump cfg/uef"_dump_cfg_uef.html +examples/uef :ul + +:line + USER-VTK package :link(USER-VTK),h4 [Contents:] diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt new file mode 100644 index 0000000000..33f847af35 --- /dev/null +++ b/doc/src/compute_temp_uef.txt @@ -0,0 +1,52 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute temp command :h3 +compute temp/kk command :h3 + +[Syntax:] + +compute ID group-ID temp :pre + +ID, group-ID are documented in "compute"_compute.html command +temp = style name of this compute command :ul + +[Examples:] + +compute 1 all temp/uef + +[Description:] + +This command is used to compute the kinetic energy tensor in +the correct reference frame when the USER-UEF package is used. +It is not necessary to use this command to compute the scalar +value of the temperature. A "compute temp"_compute_temp.html +may be used for that purpose. + +[Output info:] + +Output information for this command can be found in the +documentation for "compute temp"_compute_temp.html. + +[Restrictions:] + +This fix is part of the USER-UEF package. It is only enabled if +LAMMPS was built with that package. See the +"Making LAMMPS"_Section_start.html#start-3 section for more info. + + +This command can only be used when "fix nvt/uef"_fix_nh_uef.html +or "fix npt/uef"_fix_nh_uef.html is active. + +[Related commands:] +"compute temp"_compute_temp.html, +"fix nvt/uef"_fix_nh_uef.html, +"compute pressure/uef"_compute_pressure_uef.html + + +[Default:] none diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt new file mode 100644 index 0000000000..38d01edccf --- /dev/null +++ b/doc/src/fix_nh_uef.txt @@ -0,0 +1,715 @@ +<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix nvt/uef command :h3 +fix npt/uef command :h3 + +[Syntax:] + +fix ID group-ID style_name erate eps_x eps_y temp Tstart Tstop Tdamp keyword value ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +style_name = {nvt/uef} or {npt/uef} :l +Tstart, Tstop, and Tdamp are documented in the "fix_npt"_fix_nh.html command :l +edot_x and edot_y are the strain rates in the x and y directions (1/(time units)) :l +one or more keyword/value pairs may be appended :l +keyword = {ext} or {strain} or {iso} or {x} or {y} or {z} or {tchain} or {pchain} or {tloop} or {ploop} or {mtk} + {ext} value = {x} or {y} or {z} or {xy} or {yz} or {xz} = external dimensions + This keyword sets the external dimensions used to calculate the scalar pressure + {strain} values = e_x e_y = initial strain + Use of this keyword is usually not necessary, but may be needed to resume a run with a data file. + The {iso}, {x}, {y}, {z}, {tchain}, {pchain}, {tloop}, {ploop}, and {mtk} keywords are documented in the "fix_npt"_fix_nh.html command. :pre +:ule + +[Examples:] + +fix uniax_nvt all nvt/uef temp 400 400 100 erate 0.00001 -0.000005 +fix biax_nvt all nvt/uef temp 400 400 100 erate 0.000005 0.000005 +fix uniax_npt all npt/uef temp 400 400 300 iso 1 1 3000 erate 0.00001 -0.000005 ext yz +fix biax_npt all npt/uef temp 400 400 100 erate 0.00001 -0.000005 :pre + +[Description:] + + +This fix is used to simulate non-equilibrium molecular dynamics (NEMD) +under diagonal flow fields, including uniaxial and biaxial flow. +Simulations under extensional flow may be carried out for an +indefinite amount of time. It is an implementation of the boundary +conditions from "(Dobson)"_#Dobson, and also uses numerical lattice reduction +as was proposed by "(Hunt)"_#Hunt. The lattice reduction algorithm is from +"(Semaev)"_Semaev. The package is intended for simulations of +homogeneous flows, and integrates the SLLOD equations of motion, +originally proposed by Hoover and Ladd (see "(Evans and Morriss)"_#Sllod). + +NOTE: Due to an instability in the SLLOD equations under extension, +"fix_momentum"_fix_momentum.html should be used to regularly reset the +linear momentum. + +The boundary conditions require a simulation box that does not have a +consistent alignment relative to the applied flow field. Since LAMMPS +utilizes an upper-triangular simulation box, it is not possible to express +the evolving simulation box in the same coordinate system as the flow field. +This fix keeps track of two coordinate systems: the flow frame, and the +upper triangular LAMMPS frame. The coordinate systems are related to +each other through the QR decomposition, as is illustrated in the image below. + +image + +During most molecular dynamics operations, the system is represented in the +LAMMPS frame. Only when the positions and velocities are updated is the system +rotated to the flow frame, and it is rotated back to the LAMMPS frame +immediately afterwards. For this reason, all vector-valued quantities +(except for the tensors from compute pressure/uef and compute temp/uef) will +be computed in the LAMMPS frame. Rotationally invariant scalar quantities like +the temperature and hydrostatic pressure, on the other hand, will be computed +correctly. Additionally, the system is in the LAMMPS frame during all of the +output steps, and therefore trajectory files made using the dump command +will be in the LAMMPS frame unless the dump cfg/uef command is used. + +:line + +Temperature control is achieved with the default Nose-Hoover style +thermostat documented in "fix_npt"_fix_nh.html. When this fix is active, +only the peculiar velocity of each atom is stored, defined as the velocity +relative to the streaming velocity. This is in contrast to +"fix_nvt/sllod"_fix_nvt_sllod.html, which uses a lab-frame velocity, and +removes the contribution from the streaming velocity in order to compute +the temperature. + +Pressure control is achieved using the default Nose-Hoover barostat documented +in "fix_npt"_fix_npt.html. There are two ways to control the pressure using this +fix. The first method involves using the {ext} keyword along with the {iso} pressure +style. With this method, the pressure is controlled by scaling the simulation box +isotropically to achieve the average pressure in the directions specified by {ext}. +For example, if {ext xy} is used, the average pressure (Pxx+Pyy)/2 will be controlled. + +This command will control the total hydrostatic pressure under uniaxial tension: + +fix f1 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xyz :pre + +This command will control the average stress in compression directions, which would +correspond to free surfaces for fiber drawing, under uniaxial tension: + +fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy :pre + +The second method for pressure control involves setting the normal stresses using +the x, y , and/or z keywords. When using this method, the same pressure must be +specified via {Pstart} and {Pstop} for all dimensions controlled. Any choice of +pressure conditions that would cause LAMMPS to compute a deviatoric stress are not +permissible and will result in an error. Additionally, all dimensions with +controlled stress must have the same applied strain rate. The {ext} keyword must be +set to the default value ({xyz}) when using this method. + +For example, the following commands will work: + +fix f3 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 y 1 1 5 erate -0.5 -0.5 +fix f4 all npt/uef temp 0.7 0.7 0.5 z 1 1 5 erate 0.5 0.5 :pre + +The following commands will not work: + +fix f5 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 1 1 5 erate -0.5 -0.5 +fix f6 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 2 2 5 erate 0.5 0.5 :pre + +:line + + +[Restrictions:] + +Due to requirements of the boundary conditions, when the strain keyword +is unset, or set to zero, the initial simulation box must be cubic and +have style triclinic. If the box is initially of type ortho, use +"change_box"_change_box.html before invoking the fix. + +When this fix is applied, any orientation-dependent vector or +tensor-valued quantities computed, except for the tensors from +compute pressure/uef/compute temp/uef and coordinates from +dump cfg/uef, will not be in the same coordinate system as +the flow field. + +:link(Dobson) +[(Dobson)] Dobson, J Chem Phys, 141, 184103 (2014). + +:link(Hunt) +[(Hunt)] Hunt, Mol Simul, 42, 347 (2016). + +:link(Semaev) +[(Semaev)] Semaev, Cryptography and Lattices, 181 (2001). + +:link(Sllod) +[(Evans and Morriss)] Evans and Morriss, Phys Rev A, 30, 1528 (1984). + +These commands perform time integration on Nose-Hoover style +non-Hamiltonian equations of motion which are designed to generate +positions and velocities sampled from the canonical (nvt), +isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This +updates the position and velocity for atoms in the group each +timestep. + +The thermostatting and barostatting is achieved by adding some dynamic +variables which are coupled to the particle velocities +(thermostatting) and simulation domain dimensions (barostatting). In +addition to basic thermostatting and barostatting, these fixes can +also create a chain of thermostats coupled to the particle thermostat, +and another chain of thermostats coupled to the barostat +variables. The barostat can be coupled to the overall box volume, or +to individual dimensions, including the {xy}, {xz} and {yz} tilt +dimensions. The external pressure of the barostat can be specified as +either a scalar pressure (isobaric ensemble) or as components of a +symmetric stress tensor (constant stress ensemble). When used +correctly, the time-averaged temperature and stress tensor of the +particles will match the target values specified by Tstart/Tstop and +Pstart/Pstop. + +The equations of motion used are those of Shinoda et al in +"(Shinoda)"_#nh-Shinoda, which combine the hydrostatic equations of +Martyna, Tobias and Klein in "(Martyna)"_#nh-Martyna with the strain +energy proposed by Parrinello and Rahman in +"(Parrinello)"_#nh-Parrinello. The time integration schemes closely +follow the time-reversible measure-preserving Verlet and rRESPA +integrators derived by Tuckerman et al in "(Tuckerman)"_#nh-Tuckerman. + +:line + +The thermostat parameters for fix styles {nvt} and {npt} is specified +using the {temp} keyword. Other thermostat-related keywords are +{tchain}, {tloop} and {drag}, which are discussed below. + +The thermostat is applied to only the translational degrees of freedom +for the particles. The translational degrees of freedom can also have +a bias velocity removed before thermostatting takes place; see the +description below. The desired temperature at each timestep is a +ramped value during the run from {Tstart} to {Tstop}. The {Tdamp} +parameter is specified in time units and determines how rapidly the +temperature is relaxed. For example, a value of 10.0 means to relax +the temperature in a timespan of (roughly) 10 time units (e.g. tau or +fmsec or psec - see the "units"_units.html command). The atoms in the +fix group are the only ones whose velocities and positions are updated +by the velocity/position update portion of the integration. + +NOTE: A Nose-Hoover thermostat will not work well for arbitrary values +of {Tdamp}. If {Tdamp} is too small, the temperature can fluctuate +wildly; if it is too large, the temperature will take a very long time +to equilibrate. A good choice for many models is a {Tdamp} of around +100 timesteps. Note that this is NOT the same as 100 time units for +most "units"_units.html settings. + +:line + +The barostat parameters for fix styles {npt} and {nph} is specified +using one or more of the {iso}, {aniso}, {tri}, {x}, {y}, {z}, {xy}, +{xz}, {yz}, and {couple} keywords. These keywords give you the +ability to specify all 6 components of an external stress tensor, and +to couple various of these components together so that the dimensions +they represent are varied together during a constant-pressure +simulation. + +Other barostat-related keywords are {pchain}, {mtk}, {ploop}, +{nreset}, {drag}, and {dilate}, which are discussed below. + +Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). +Triclinic (non-orthogonal) simulation boxes have 6 adjustable +dimensions (x,y,z,xy,xz,yz). The "create_box"_create_box.html, "read +data"_read_data.html, and "read_restart"_read_restart.html commands +specify whether the simulation box is orthogonal or non-orthogonal +(triclinic) and explain the meaning of the xy,xz,yz tilt factors. + +The target pressures for each of the 6 components of the stress tensor +can be specified independently via the {x}, {y}, {z}, {xy}, {xz}, {yz} +keywords, which correspond to the 6 simulation box dimensions. For +each component, the external pressure or tensor component at each +timestep is a ramped value during the run from {Pstart} to {Pstop}. +If a target pressure is specified for a component, then the +corresponding box dimension will change during a simulation. For +example, if the {y} keyword is used, the y-box length will change. If +the {xy} keyword is used, the xy tilt factor will change. A box +dimension will not change if that component is not specified, although +you have the option to change that dimension via the "fix +deform"_fix_deform.html command. + +Note that in order to use the {xy}, {xz}, or {yz} keywords, the +simulation box must be triclinic, even if its initial tilt factors are +0.0. + +For all barostat keywords, the {Pdamp} parameter operates like the +{Tdamp} parameter, determining the time scale on which pressure is +relaxed. For example, a value of 10.0 means to relax the pressure in +a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see +the "units"_units.html command). + +NOTE: A Nose-Hoover barostat will not work well for arbitrary values +of {Pdamp}. If {Pdamp} is too small, the pressure and volume can +fluctuate wildly; if it is too large, the pressure will take a very +long time to equilibrate. A good choice for many models is a {Pdamp} +of around 1000 timesteps. However, note that {Pdamp} is specified in +time units, and that timesteps are NOT the same as time units for most +"units"_units.html settings. + +Regardless of what atoms are in the fix group (the only atoms which +are time integrated), a global pressure or stress tensor is computed +for all atoms. Similarly, when the size of the simulation box is +changed, all atoms are re-scaled to new positions, unless the keyword +{dilate} is specified with a {dilate-group-ID} for a group that +represents a subset of the atoms. This can be useful, for example, to +leave the coordinates of atoms in a solid substrate unchanged and +controlling the pressure of a surrounding fluid. This option should +be used with care, since it can be unphysical to dilate some atoms and +not others, because it can introduce large, instantaneous +displacements between a pair of atoms (one dilated, one not) that are +far from the dilation origin. Also note that for atoms not in the fix +group, a separate time integration fix like "fix nve"_fix_nve.html or +"fix nvt"_fix_nh.html can be used on them, independent of whether they +are dilated or not. + +:line + +The {couple} keyword allows two or three of the diagonal components of +the pressure tensor to be "coupled" together. The value specified +with the keyword determines which are coupled. For example, {xz} +means the {Pxx} and {Pzz} components of the stress tensor are coupled. +{Xyz} means all 3 diagonal components are coupled. Coupling means two +things: the instantaneous stress will be computed as an average of the +corresponding diagonal components, and the coupled box dimensions will +be changed together in lockstep, meaning coupled dimensions will be +dilated or contracted by the same percentage every timestep. The +{Pstart}, {Pstop}, {Pdamp} parameters for any coupled dimensions must +be identical. {Couple xyz} can be used for a 2d simulation; the {z} +dimension is simply ignored. + +:line + +The {iso}, {aniso}, and {tri} keywords are simply shortcuts that are +equivalent to specifying several other keywords together. + +The keyword {iso} means couple all 3 diagonal components together when +pressure is computed (hydrostatic pressure), and dilate/contract the +dimensions together. Using "iso Pstart Pstop Pdamp" is the same as +specifying these 4 keywords: + +x Pstart Pstop Pdamp +y Pstart Pstop Pdamp +z Pstart Pstop Pdamp +couple xyz :pre + +The keyword {aniso} means {x}, {y}, and {z} dimensions are controlled +independently using the {Pxx}, {Pyy}, and {Pzz} components of the +stress tensor as the driving forces, and the specified scalar external +pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying +these 4 keywords: + +x Pstart Pstop Pdamp +y Pstart Pstop Pdamp +z Pstart Pstop Pdamp +couple none :pre + +The keyword {tri} means {x}, {y}, {z}, {xy}, {xz}, and {yz} dimensions +are controlled independently using their individual stress components +as the driving forces, and the specified scalar pressure as the +external normal stress. Using "tri Pstart Pstop Pdamp" is the same as +specifying these 7 keywords: + +x Pstart Pstop Pdamp +y Pstart Pstop Pdamp +z Pstart Pstop Pdamp +xy 0.0 0.0 Pdamp +yz 0.0 0.0 Pdamp +xz 0.0 0.0 Pdamp +couple none :pre + +:line + +In some cases (e.g. for solids) the pressure (volume) and/or +temperature of the system can oscillate undesirably when a Nose/Hoover +barostat and thermostat is applied. The optional {drag} keyword will +damp these oscillations, although it alters the Nose/Hoover equations. +A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged. +A non-zero value adds a drag term; the larger the value specified, the +greater the damping effect. Performing a short run and monitoring the +pressure and temperature is the best way to determine if the drag term +is working. Typically a value between 0.2 to 2.0 is sufficient to +damp oscillations after a few periods. Note that use of the drag +keyword will interfere with energy conservation and will also change +the distribution of positions and velocities so that they do not +correspond to the nominal NVT, NPT, or NPH ensembles. + +An alternative way to control initial oscillations is to use chain +thermostats. The keyword {tchain} determines the number of thermostats +in the particle thermostat. A value of 1 corresponds to the original +Nose-Hoover thermostat. The keyword {pchain} specifies the number of +thermostats in the chain thermostatting the barostat degrees of +freedom. A value of 0 corresponds to no thermostatting of the +barostat variables. + +The {mtk} keyword controls whether or not the correction terms due to +Martyna, Tuckerman, and Klein are included in the equations of motion +"(Martyna)"_#nh-Martyna. Specifying {no} reproduces the original +Hoover barostat, whose volume probability distribution function +differs from the true NPT and NPH ensembles by a factor of 1/V. Hence +using {yes} is more correct, but in many cases the difference is +negligible. + +The keyword {tloop} can be used to improve the accuracy of integration +scheme at little extra cost. The initial and final updates of the +thermostat variables are broken up into {tloop} substeps, each of +length {dt}/{tloop}. This corresponds to using a first-order +Suzuki-Yoshida scheme "(Tuckerman)"_#nh-Tuckerman. The keyword {ploop} +does the same thing for the barostat thermostat. + +The keyword {nreset} controls how often the reference dimensions used +to define the strain energy are reset. If this keyword is not used, +or is given a value of zero, then the reference dimensions are set to +those of the initial simulation domain and are never changed. If the +simulation domain changes significantly during the simulation, then +the final average pressure tensor will differ significantly from the +specified values of the external stress tensor. A value of {nstep} +means that every {nstep} timesteps, the reference dimensions are set +to those of the current simulation domain. + +The {scaleyz}, {scalexz}, and {scalexy} keywords control whether or +not the corresponding tilt factors are scaled with the associated box +dimensions when barostatting triclinic periodic cells. The default +values {yes} will turn on scaling, which corresponds to adjusting the +linear dimensions of the cell while preserving its shape. Choosing +{no} ensures that the tilt factors are not scaled with the box +dimensions. See below for restrictions and default values in different +situations. In older versions of LAMMPS, scaling of tilt factors was +not performed. The old behavior can be recovered by setting all three +scale keywords to {no}. + +The {flip} keyword allows the tilt factors for a triclinic box to +exceed half the distance of the parallel box length, as discussed +below. If the {flip} value is set to {yes}, the bound is enforced by +flipping the box when it is exceeded. If the {flip} value is set to +{no}, the tilt will continue to change without flipping. Note that if +applied stress induces large deformations (e.g. in a liquid), this +means the box shape can tilt dramatically and LAMMPS will run less +efficiently, due to the large volume of communication needed to +acquire ghost atoms around a processor's irregular-shaped sub-domain. +For extreme values of tilt, LAMMPS may also lose atoms and generate an +error. + +The {fixedpoint} keyword specifies the fixed point for barostat volume +changes. By default, it is the center of the box. Whatever point is +chosen will not move during the simulation. For example, if the lower +periodic boundaries pass through (0,0,0), and this point is provided +to {fixedpoint}, then the lower periodic boundaries will remain at +(0,0,0), while the upper periodic boundaries will move twice as +far. In all cases, the particle trajectories are unaffected by the +chosen value, except for a time-dependent constant translation of +positions. + +If the {update} keyword is used with the {dipole} value, then the +orientation of the dipole moment of each particle is also updated +during the time integration. This option should be used for models +where a dipole moment is assigned to finite-size particles, +e.g. spheroids via use of the "atom_style hybrid sphere +dipole"_atom_style.html command. + +The default dipole orientation integrator can be changed to the +Dullweber-Leimkuhler-McLachlan integration scheme +"(Dullweber)"_#nh-Dullweber when using {update} with the value +{dipole/dlm}. This integrator is symplectic and time-reversible, +giving better energy conservation and allows slightly longer timesteps +at only a small additional computational cost. + +:line + +NOTE: Using a barostat coupled to tilt dimensions {xy}, {xz}, {yz} can +sometimes result in arbitrarily large values of the tilt dimensions, +i.e. a dramatically deformed simulation box. LAMMPS allows the tilt +factors to grow a small amount beyond the normal limit of half the box +length (0.6 times the box length), and then performs a box "flip" to +an equivalent periodic cell. See the discussion of the {flip} keyword +above, to allow this bound to be exceeded, if desired. + +The flip operation is described in more detail in the doc page for +"fix deform"_fix_deform.html. Both the barostat dynamics and the atom +trajectories are unaffected by this operation. However, if a tilt +factor is incremented by a large amount (1.5 times the box length) on +a single timestep, LAMMPS can not accomodate this event and will +terminate the simulation with an error. This error typically indicates +that there is something badly wrong with how the simulation was +constructed, such as specifying values of {Pstart} that are too far +from the current stress value, or specifying a timestep that is too +large. Triclinic barostatting should be used with care. This also is +true for other barostat styles, although they tend to be more +forgiving of insults. In particular, it is important to recognize that +equilibrium liquids can not support a shear stress and that +equilibrium solids can not support shear stresses that exceed the +yield stress. + +One exception to this rule is if the 1st dimension in the tilt factor +(x for xy) is non-periodic. In that case, the limits on the tilt +factor are not enforced, since flipping the box in that dimension does +not change the atom positions due to non-periodicity. In this mode, +if you tilt the system to extreme angles, the simulation will simply +become inefficient due to the highly skewed simulation box. + +NOTE: Unlike the "fix temp/berendsen"_fix_temp_berendsen.html command +which performs thermostatting but NO time integration, these fixes +perform thermostatting/barostatting AND time integration. Thus you +should not use any other time integration fix, such as "fix +nve"_fix_nve.html on atoms to which this fix is applied. Likewise, +fix nvt and fix npt should not normally be used on atoms that also +have their temperature controlled by another fix - e.g. by "fix +langevin"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html +commands. + +See "this howto section"_Section_howto.html#howto_16 of the manual for +a discussion of different ways to compute temperature and perform +thermostatting and barostatting. + +:line + +These fixes compute a temperature and pressure each timestep. To do +this, the fix creates its own computes of style "temp" and "pressure", +as if one of these two sets of commands had been issued: + +compute fix-ID_temp group-ID temp +compute fix-ID_press group-ID pressure fix-ID_temp :pre + +compute fix-ID_temp all temp +compute fix-ID_press all pressure fix-ID_temp :pre + +See the "compute temp"_compute_temp.html and "compute +pressure"_compute_pressure.html commands for details. Note that the +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID ++ underscore + "press". For fix nvt, the group for the new computes +is the same as the fix group. For fix nph and fix npt, the group for +the new computes is "all" since pressure is computed for the entire +system. + +Note that these are NOT the computes used by thermodynamic output (see +the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} +and {thermo_press}. This means you can change the attributes of this +fix's temperature or pressure via the +"compute_modify"_compute_modify.html command or print this temperature +or pressure during thermodynamic output via the "thermo_style +custom"_thermo_style.html command using the appropriate compute-ID. +It also means that changing attributes of {thermo_temp} or +{thermo_press} will have no effect on this fix. + +Like other fixes that perform thermostatting, fix nvt and fix npt can +be used with "compute commands"_compute.html that calculate a +temperature after removing a "bias" from the atom velocities. +E.g. removing the center-of-mass velocity from a group of atoms or +only calculating temperature on the x-component of velocity or only +calculating temperature for atoms in a geometric region. This is not +done by default, but only if the "fix_modify"_fix_modify.html command +is used to assign a temperature compute to this fix that includes such +a bias term. See the doc pages for individual "compute +commands"_compute.html to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + +:line + +These fixes can be used with either the {verlet} or {respa} +"integrators"_run_style.html. When using one of the barostat fixes +with {respa}, LAMMPS uses an integrator constructed +according to the following factorization of the Liouville propagator +(for two rRESPA levels): + +:c,image(Eqs/fix_nh1.jpg) + +This factorization differs somewhat from that of Tuckerman et al, in +that the barostat is only updated at the outermost rRESPA level, +whereas Tuckerman's factorization requires splitting the pressure into +pieces corresponding to the forces computed at each rRESPA level. In +theory, the latter method will exhibit better numerical stability. In +practice, because Pdamp is normally chosen to be a large multiple of +the outermost rRESPA timestep, the barostat dynamics are not the +limiting factor for numerical stability. Both factorizations are +time-reversible and can be shown to preserve the phase space measure +of the underlying non-Hamiltonian equations of motion. + +NOTE: This implementation has been shown to conserve linear momentum +up to machine precision under NVT dynamics. Under NPT dynamics, +for a system with zero initial total linear momentum, the total +momentum fluctuates close to zero. It may occasionally undergo brief +excursions to non-negligible values, before returning close to zero. +Over long simulations, this has the effect of causing the center-of-mass +to undergo a slow random walk. This can be mitigated by resetting +the momentum at infrequent intervals using the +"fix momentum"_fix_momentum.html command. + +:line + +The fix npt and fix nph commands can be used with rigid bodies or +mixtures of rigid bodies and non-rigid particles (e.g. solvent). But +there are also "fix rigid/npt"_fix_rigid.html and "fix +rigid/nph"_fix_rigid.html commands, which are typically a more natural +choice. See the doc page for those commands for more discussion of +the various ways to do this. + +:line + +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 in "Section 5"_Section_accelerate.html +of the manual. 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 "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the "-suffix command-line +switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +use the "suffix"_suffix.html command in your input script. + +See "Section 5"_Section_accelerate.html of the manual for +more instructions on how to use the accelerated styles effectively. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +These fixes writes the state of all the thermostat and barostat +variables to "binary restart files"_restart.html. See the +"read_restart"_read_restart.html command for info on how to re-specify +a fix in an input script that reads a restart file, so that the +operation of the fix continues in an uninterrupted fashion. + +The "fix_modify"_fix_modify.html {temp} and {press} options are +supported by these fixes. You can use them to assign a +"compute"_compute.html you have defined to this fix which will be used +in its thermostatting or barostatting procedure, as described above. +If you do this, note that the kinetic energy derived from the compute +temperature should be consistent with the virial term computed using +all atoms for the pressure. LAMMPS will warn you if you choose to +compute temperature on a subset of atoms. + +NOTE: If both the {temp} and {press} keywords are used in a single +thermo_modify command (or in two separate commands), then the order in +which the keywords are specified is important. Note that a "pressure +compute"_compute_pressure.html defines its own temperature compute as +an argument when it is specified. The {temp} keyword will override +this (for the pressure compute being used by fix npt), but only if the +{temp} keyword comes after the {press} keyword. If the {temp} keyword +comes before the {press} keyword, then the new pressure compute +specified by the {press} keyword will be unaffected by the {temp} +setting. + +The "fix_modify"_fix_modify.html {energy} option is supported by these +fixes to add the energy change induced by Nose/Hoover thermostatting +and barostatting to the system's potential energy as part of +"thermodynamic output"_thermo_style.html. + +These fixes compute a global scalar and a global vector of quantities, +which can be accessed by various "output +commands"_Section_howto.html#howto_15. The scalar value calculated by +these fixes is "extensive"; the vector values are "intensive". + +The scalar is the cumulative energy change due to the fix. + +The vector stores internal Nose/Hoover thermostat and barostat +variables. The number and meaning of the vector values depends on +which fix is used and the settings for keywords {tchain} and {pchain}, +which specify the number of Nose/Hoover chains for the thermostat and +barostat. If no thermostatting is done, then {tchain} is 0. If no +barostatting is done, then {pchain} is 0. In the following list, +"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in +the barostat. Its value is 0 if no barostat is used, else its value +is 6 if any off-diagonal stress tensor component is barostatted, else +its value is 1 if {couple xyz} is used or {couple xy} for a 2d +simulation, otherwise its value is 3. + +The order of values in the global vector and their meaning is as +follows. The notation means there are tchain values for eta, followed +by tchain for eta_dot, followed by ndof for omega, etc: + +eta\[tchain\] = particle thermostat displacements (unitless) +eta_dot\[tchain\] = particle thermostat velocities (1/time units) +omega\[ndof\] = barostat displacements (unitless) +omega_dot\[ndof\] = barostat velocities (1/time units) +etap\[pchain\] = barostat thermostat displacements (unitless) +etap_dot\[pchain\] = barostat thermostat velocities (1/time units) +PE_eta\[tchain\] = potential energy of each particle thermostat displacement (energy units) +KE_eta_dot\[tchain\] = kinetic energy of each particle thermostat velocity (energy units) +PE_omega\[ndof\] = potential energy of each barostat displacement (energy units) +KE_omega_dot\[ndof\] = kinetic energy of each barostat velocity (energy units) +PE_etap\[pchain\] = potential energy of each barostat thermostat displacement (energy units) +KE_etap_dot\[pchain\] = kinetic energy of each barostat thermostat velocity (energy units) +PE_strain\[1\] = scalar strain energy (energy units) :ul + +These fixes can ramp their external temperature and pressure over +multiple runs, using the {start} and {stop} keywords of the +"run"_run.html command. See the "run"_run.html command for details of +how to do this. + +These fixes are not invoked during "energy +minimization"_minimize.html. + +:line + +[Restrictions:] + +{X}, {y}, {z} cannot be barostatted if the associated dimension is not +periodic. {Xy}, {xz}, and {yz} can only be barostatted if the +simulation domain is triclinic and the 2nd dimension in the keyword +({y} dimension in {xy}) is periodic. {Z}, {xz}, and {yz}, cannot be +barostatted for 2D simulations. The "create_box"_create_box.html, +"read data"_read_data.html, and "read_restart"_read_restart.html +commands specify whether the simulation box is orthogonal or +non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz +tilt factors. + +For the {temp} keyword, the final Tstop cannot be 0.0 since it would +make the external T = 0.0 at some timestep during the simulation which +is not allowed in the Nose/Hoover formulation. + +The {scaleyz yes} and {scalexz yes} keyword/value pairs can not be used +for 2D simulations. {scaleyz yes}, {scalexz yes}, and {scalexy yes} options +can only be used if the 2nd dimension in the keyword is periodic, +and if the tilt factor is not coupled to the barostat via keywords +{tri}, {yz}, {xz}, and {xy}. + +These fixes can be used with dynamic groups as defined by the +"group"_group.html command. Likewise they can be used with groups to +which atoms are added or deleted over time, e.g. a deposition +simulation. However, the conservation properties of the thermostat +and barostat are defined for systems with a static set of atoms. You +may observe odd behavior if the atoms in a group vary dramatically +over time or the atom count becomes very small. + +[Related commands:] + +"fix nve"_fix_nve.html, "fix_modify"_fix_modify.html, +"run_style"_run_style.html + +[Default:] + +The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = +ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none, +scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and +not coupled to barostat, otherwise no. + +:line + +:link(nh-Martyna) +[(Martyna)] Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). + +:link(nh-Parrinello) +[(Parrinello)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). + +:link(nh-Tuckerman) +[(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and +Martyna, J Phys A: Math Gen, 39, 5629 (2006). + +:link(nh-Shinoda) +[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). + +:link(nh-Dullweber) +[(Dullweber)] Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, +5840 (1997). diff --git a/examples/USER/uef/README b/examples/USER/uef/README new file mode 100644 index 0000000000..aaf53fa2a1 --- /dev/null +++ b/examples/USER/uef/README @@ -0,0 +1,19 @@ +This directory contains two short example scripts for the USER-UEF +package. + + +nvt_uniaxial: + A simulation of a WCA fluid under constant volume uniaxial strain + with stretching in the z direction, compression in the x and y + directions.The xx, yy and zz components of the pressure tensor are + written to the log file. The simulation conditions are the same + used in the paper by Thomas Hunt [http://arxiv.org/abs/1310.3905] + and should yield an zz pressure near 5 and xx/yy pressures near 10. + +npt_biaxial: + A simulation of a WCA fluid under stress-controlled biaxial strain + with stretching in the x and y directions, compression in the z + direction. The zz stress is controlled using the ext keyword in fix + npt/uef. The xx yy and zz components of the pressure tensor are + written to the log file. The simulations conditions should yield + xx/yy pressures near 5 and zz pressure near 10 diff --git a/examples/USER/uef/npt_biaxial/data.wca b/examples/USER/uef/npt_biaxial/data.wca new file mode 100644 index 0000000000..889ba4d2f2 --- /dev/null +++ b/examples/USER/uef/npt_biaxial/data.wca @@ -0,0 +1,1022 @@ +LAMMPS data file via write_data, version 14 May 2016, timestep = 400000 + +500 atoms +1 atom types + +0.0000000000000000e+00 8.3979809569125372e+00 xlo xhi +0.0000000000000000e+00 8.3979809569125372e+00 ylo yhi +0.0000000000000000e+00 8.3979809569125372e+00 zlo zhi + +Masses + +1 1 + +Pair Coeffs # lj/cut + +1 1 1 + +Atoms # atomic + +7 1 2.4137737201272674e-01 2.0017433398687118e-01 3.6157393311703534e-02 2 1 2 +398 1 1.6739594898193126e+00 3.0313452824803544e-01 5.7986723161362197e-01 -3 0 1 +173 1 6.1370793327804556e+00 4.4978954867119525e-01 3.6568951377817088e-01 -4 1 0 +462 1 7.8754716784931862e+00 5.2908038473333074e-01 7.9185633743762940e-01 1 1 -2 +383 1 6.5373096080170212e-01 1.5337525983981986e+00 6.3208419126059423e-01 2 0 1 +288 1 1.9354124990672374e+00 1.3318105136786291e+00 3.6211635210084403e-01 -1 1 0 +303 1 2.9661308460819318e+00 1.1444058564802859e+00 6.5604777151148241e-01 -2 2 1 +491 1 7.1514675802966758e+00 1.3588685826107376e+00 1.2875068928885325e-01 -1 0 0 +187 1 3.0670386025081497e-01 2.4850915964494620e+00 7.0944157374329464e-02 0 -1 0 +163 1 1.2805212773629451e+00 2.4034621328433090e+00 2.0184086197146742e-01 0 1 -1 +345 1 2.5952244948945173e+00 2.3405536448220743e+00 3.0019149048630317e-01 -3 2 1 +447 1 3.9059163101716741e+00 1.6849179478858272e+00 6.0306488750926446e-01 -2 3 -4 +108 1 4.9215629854759335e+00 2.5174843149522088e+00 6.2779912940916158e-02 1 0 -1 +427 1 6.3978861821382305e+00 1.9201774263431104e+00 4.3981049730412797e-01 -1 -2 -3 +96 1 7.4061541304605534e+00 2.4828308207907996e+00 2.4705543772216432e-01 0 -3 2 +494 1 8.0759482343563711e+00 1.6914241739458744e+00 6.8482420189075921e-01 -3 1 2 +360 1 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-1.4405372913769463e+00 -1.2161267905238037e-01 -7.1275775203655271e-03 +66 -2.2455608800065441e-01 -5.5194985983545303e-02 -2.9031971555487707e-01 +371 2.8693892522161785e-01 -1.3942754264578394e-01 4.1638095135795372e-01 +186 -2.5542578648985415e-01 -2.7435394726950046e-01 1.6931522427410683e+00 +413 5.6007135922818607e-01 1.2189064363493711e-01 -7.5271223366515216e-01 diff --git a/examples/USER/uef/npt_biaxial/in.npt_biaxial b/examples/USER/uef/npt_biaxial/in.npt_biaxial new file mode 100644 index 0000000000..152054fce6 --- /dev/null +++ b/examples/USER/uef/npt_biaxial/in.npt_biaxial @@ -0,0 +1,31 @@ +# biaxial NPT deformation of WCA fluid + +units lj +atom_style atomic + + +pair_style lj/cut 1.122562 +read_data data.wca +pair_coeff 1 1 1.0 1.0 +pair_modify shift yes + +neighbor 0.5 bin +neigh_modify delay 0 + +change_box all triclinic + +# these commads show the different methods that may be used to impose +# a constant stress through isotropic or anisotropic coupling +fix 1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z +#fix 1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5 erate 0.5 0.5 ext xyz + +fix 2 all momentum 100 linear 1 1 1 + +#dump 1 all atom 25 dump.lammpstrj + +#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs + +thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] + +thermo 50 +run 10000 diff --git a/examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.1 b/examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.1 new file mode 100644 index 0000000000..65f0184d13 --- /dev/null +++ b/examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.1 @@ -0,0 +1,276 @@ +LAMMPS (30 Jul 2016) +# biaxial NPT deformation of WCA fluid + +units lj +atom_style atomic + + +pair_style lj/cut 1.122562 +read_data data.wca + orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities +pair_coeff 1 1 1.0 1.0 +pair_modify shift yes + +neighbor 0.5 bin +neigh_modify delay 0 + +change_box all triclinic + triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) + +# these commads show the different methods that may be used to impose +# a constant stress through isotropic or anisotropic coupling +fix 1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z +#fix 1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5 erate 0.5 0.5 ext xyz + +fix 2 all momentum 100 linear 1 1 1 + +#dump 1 all atom 25 dump.lammpstrj + +#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs + +thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] + +thermo 50 +run 10000 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.62256 + ghost atom cutoff = 1.62256 + binsize = 0.811281 -> bins = 11 11 11 +Memory usage per processor = 2.40217 Mbytes +Step 1_press[ 1_press[ 1_press[ + 0 6.3937851 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8.3815668 + 4150 4.8060033 4.3415868 9.6553386 + 4200 4.8548303 4.8006768 9.5995801 + 4250 5.0976366 5.2683175 10.386444 + 4300 5.8921937 5.5134696 10.788143 + 4350 5.8323871 5.5255869 11.199128 + 4400 5.2464655 5.0005905 10.311055 + 4450 4.9264849 5.2499854 10.26702 + 4500 4.4431895 4.536981 8.7489096 + 4550 4.5180914 4.2080277 8.6525529 + 4600 5.1782188 5.1224059 10.683341 + 4650 5.4156233 4.8714464 10.473939 + 4700 5.3107669 5.224614 10.569391 + 4750 4.9538022 5.2509475 10.288918 + 4800 4.6976945 4.8107142 9.8299772 + 4850 5.1227936 5.0737571 10.440452 + 4900 4.7580514 4.6375995 9.1971008 + 4950 5.0647601 4.6470735 9.583131 + 5000 5.196231 5.7531491 10.409807 + 5050 5.6691323 5.7163652 12.335701 + 5100 5.3603738 5.4887106 10.961712 + 5150 4.455028 4.6494465 9.8096968 + 5200 4.7596912 4.4804896 9.3762885 + 5250 5.3144927 5.0113772 9.553101 + 5300 5.3445266 4.8262035 9.1220802 + 5350 5.1540657 5.5982676 10.765178 + 5400 5.1773418 5.2684381 10.452351 + 5450 4.8946859 5.3283747 9.8015564 + 5500 5.2009608 4.7183522 9.4558009 + 5550 5.4158589 5.5005458 10.539505 + 5600 4.7196831 5.4181991 9.6439249 + 5650 4.8333571 4.8601728 8.9350189 + 5700 5.4395698 4.9730096 10.669681 + 5750 5.2947443 5.6973259 10.020539 + 5800 5.4391993 5.5255143 10.264969 + 5850 4.9921388 5.2643827 10.217028 + 5900 5.0048643 4.7952641 8.9718929 + 5950 5.1843818 4.5987295 9.6858944 + 6000 5.0343993 4.946933 9.7436708 + 6050 4.6202714 5.3502658 10.752915 + 6100 5.6914422 5.3621964 10.281827 + 6150 5.1928763 5.9652686 10.923881 + 6200 5.0030409 5.2013891 10.056308 + 6250 4.9699876 5.2363753 9.9964211 + 6300 4.9129606 4.4558458 9.0419952 + 6350 4.6623958 4.4078264 8.528649 + 6400 4.9811441 5.1183207 10.261751 + 6450 5.3644017 5.5153937 10.401295 + 6500 5.6674981 5.7427566 11.928777 + 6550 5.1622364 5.3212928 10.067198 + 6600 4.5954278 5.1645397 10.16724 + 6650 4.9192712 5.0413326 9.95656 + 6700 4.6179845 4.5656214 9.3798952 + 6750 4.7287495 4.5071148 8.7890116 + 6800 4.8600442 4.8083512 10.245595 + 6850 5.0515531 5.1609272 10.553855 + 6900 5.1159742 5.1359869 10.594699 + 6950 4.8908884 5.0592418 9.5698704 + 7000 4.7654136 4.7530776 8.9439321 + 7050 4.779293 4.7534957 9.7244349 + 7100 5.2265831 5.6869073 10.32717 + 7150 5.4019177 5.15174 10.457567 + 7200 4.9817102 5.0596098 10.337574 + 7250 5.1836654 5.6065238 10.723108 + 7300 4.2916569 4.457143 8.5419099 + 7350 4.3906104 4.5439294 9.0805415 + 7400 4.998572 5.3386063 10.491418 + 7450 5.1109022 5.0506801 10.636116 + 7500 5.0248381 5.019932 10.217023 + 7550 5.0109265 5.1438717 9.9032426 + 7600 4.6628614 4.6204146 8.9459669 + 7650 4.8930717 5.0650009 10.049331 + 7700 4.9373454 5.6265835 10.210644 + 7750 5.5001067 5.3133253 10.667995 + 7800 5.0816102 5.0125753 10.591986 + 7850 4.9638046 5.1969015 9.9728333 + 7900 4.8438207 4.9217213 8.9978809 + 7950 4.7318805 4.6248537 8.6806596 + 8000 5.2808543 5.2892613 10.932535 + 8050 5.9609722 5.87087 10.47602 + 8100 5.2190231 5.6693244 11.244536 + 8150 5.3481127 5.2849903 10.222845 + 8200 4.7833053 4.7404657 9.2034474 + 8250 4.5461994 4.510467 10.294452 + 8300 4.6025175 4.8332817 8.7967546 + 8350 5.0389897 5.6642908 10.243402 + 8400 4.8414338 4.8925143 9.3653631 + 8450 5.5087429 4.7830361 10.831666 + 8500 5.2678146 5.1697789 9.9105782 + 8550 5.1211843 4.9097801 9.4165956 + 8600 5.8239149 5.0821022 10.803261 + 8650 5.3620154 5.5831747 11.16202 + 8700 5.1625813 4.8791404 10.537681 + 8750 4.5622461 5.0157549 10.013227 + 8800 4.4051517 5.0224553 9.6364273 + 8850 4.1711629 4.635617 8.5470244 + 8900 4.7049907 5.2458435 10.100728 + 8950 4.8568883 5.2360772 9.2306469 + 9000 5.0091899 5.2203574 10.718541 + 9050 5.1037824 4.9022451 10.24271 + 9100 5.0789015 4.9331454 9.173614 + 9150 5.3865455 5.3427553 11.40199 + 9200 5.5089482 5.9423232 10.976063 + 9250 5.1353552 5.0650262 10.040607 + 9300 4.6761948 4.9155175 9.6413722 + 9350 4.4780834 4.3934708 8.7049819 + 9400 4.2561799 4.7906324 9.046134 + 9450 5.6162819 5.2881846 9.9040868 + 9500 5.7554547 5.6111262 10.23849 + 9550 5.4230462 5.5656045 10.908006 + 9600 5.5045685 4.9818892 9.8929535 + 9650 5.0541481 5.0183351 9.5226021 + 9700 4.9712829 5.2395398 9.9996693 + 9750 5.0960017 5.4419775 10.914719 + 9800 5.0790688 5.6378474 10.00789 + 9850 4.9661747 5.114502 9.4585052 + 9900 5.0133498 4.7456254 9.4572653 + 9950 5.3318846 4.6643122 10.096292 + 10000 5.2227687 4.8924305 9.5894615 +Loop time of 4.42114 on 1 procs for 10000 steps with 500 atoms + +Performance: 977122.661 tau/day, 2261.858 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.72321 | 0.72321 | 0.72321 | 0.0 | 16.36 +Neigh | 2.6161 | 2.6161 | 2.6161 | 0.0 | 59.17 +Comm | 0.30217 | 0.30217 | 0.30217 | 0.0 | 6.83 +Output | 0.0034378 | 0.0034378 | 0.0034378 | 0.0 | 0.08 +Modify | 0.67004 | 0.67004 | 0.67004 | 0.0 | 15.16 +Other | | 0.1062 | | | 2.40 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 905 ave 905 max 905 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3340 ave 3340 max 3340 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3340 +Ave neighs/atom = 6.68 +Neighbor list builds = 4580 +Dangerous builds = 0 +Total wall time: 0:00:04 diff --git a/examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.4 b/examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.4 new file mode 100644 index 0000000000..4ff3551605 --- /dev/null +++ b/examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.4 @@ -0,0 +1,276 @@ +LAMMPS (30 Jul 2016) +# biaxial NPT deformation of WCA fluid + +units lj +atom_style atomic + + +pair_style lj/cut 1.122562 +read_data data.wca + orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities +pair_coeff 1 1 1.0 1.0 +pair_modify shift yes + +neighbor 0.5 bin +neigh_modify delay 0 + +change_box all triclinic + triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) + +# these commads show the different methods that may be used to impose +# a constant stress through isotropic or anisotropic coupling +fix 1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z +#fix 1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5 erate 0.5 0.5 ext xyz + +fix 2 all momentum 100 linear 1 1 1 + +#dump 1 all atom 25 dump.lammpstrj + +#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs + +thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] + +thermo 50 +run 10000 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.62256 + ghost atom cutoff = 1.62256 + binsize = 0.811281 -> bins = 11 11 11 +Memory usage per processor = 2.38201 Mbytes +Step 1_press[ 1_press[ 1_press[ + 0 6.3937851 7.0436438 6.4461087 + 50 7.9020345 7.303289 14.733929 + 100 8.3214325 8.385843 13.166247 + 150 5.7168419 5.6083988 9.7224198 + 200 3.8875348 4.0840705 7.9912973 + 250 4.2933724 4.2410519 7.7200953 + 300 4.5452314 4.2434949 8.6709832 + 350 5.446489 5.6166962 11.300536 + 400 6.0682558 5.7787878 12.106852 + 450 5.3884296 5.5066688 9.9100012 + 500 4.8046418 4.7115986 9.9769201 + 550 4.9043933 4.6240966 9.319336 + 600 4.6843238 4.9571246 9.5325487 + 650 5.1952989 5.195648 9.6187047 + 700 5.4163364 5.2938289 10.136655 + 750 5.6723178 5.0670261 11.415221 + 800 5.9379901 5.6402916 10.815209 + 850 5.0695389 5.3021432 10.742859 + 900 4.6498961 4.7111912 9.8453525 + 950 4.4811637 5.170132 9.4217644 + 1000 4.7501491 4.2420769 9.3510789 + 1050 4.5973375 5.2046786 9.8633021 + 1100 4.7879517 4.905134 9.8658575 + 1150 5.0528775 5.5048673 10.110907 + 1200 4.9926837 5.2482072 9.961051 + 1250 4.8475661 4.8499052 9.5753719 + 1300 5.2929874 5.0593404 10.869345 + 1350 5.4722108 5.083063 10.693408 + 1400 4.816304 4.9851244 10.041255 + 1450 4.6280905 4.5646059 9.2298768 + 1500 5.01985 4.5471327 8.721625 + 1550 4.8741077 5.1549887 10.256565 + 1600 5.4916921 5.3197646 10.281538 + 1650 5.4772243 5.1837045 9.9982297 + 1700 4.9419503 5.2869766 9.5825456 + 1750 5.0000465 4.6358961 8.8873809 + 1800 5.0008968 4.9755404 10.274347 + 1850 5.3911106 5.0602442 10.252838 + 1900 5.6306791 5.5982927 11.287727 + 1950 5.0117663 4.9037147 9.9079668 + 2000 4.9080829 4.8206128 9.2645313 + 2050 4.7794302 4.5942332 9.22621 + 2100 5.1197536 4.884078 9.9557557 + 2150 5.5674448 4.9602998 10.825168 + 2200 5.9993278 5.484917 11.201052 + 2250 5.619781 5.2475017 10.382149 + 2300 4.7213112 4.5460993 10.254176 + 2350 4.4310098 4.6363048 8.2696199 + 2400 4.2798177 4.1485611 8.2037599 + 2450 5.0414399 5.2572888 10.126969 + 2500 5.2807077 5.4633007 10.424033 + 2550 5.4538601 5.3268172 10.06153 + 2600 4.9750473 5.2268468 10.433373 + 2650 4.8397032 5.2258654 9.8686538 + 2700 4.8943282 4.7637421 9.8715146 + 2750 4.8870682 4.7334316 9.2096451 + 2800 4.7611053 4.9820018 9.0797655 + 2850 4.826047 5.2478652 10.549013 + 2900 5.5999506 5.0160442 9.6169413 + 2950 5.6210454 5.1519961 10.23173 + 3000 5.2132243 5.1449194 9.9778889 + 3050 5.651798 5.5919186 10.772823 + 3100 4.8453492 4.6559497 9.175617 + 3150 4.359467 4.9901271 8.512659 + 3200 4.5724772 4.8788065 9.2580198 + 3250 5.3195893 5.6518901 10.562311 + 3300 5.4571458 5.9778537 11.804991 + 3350 5.1322763 5.280149 10.894715 + 3400 4.9393514 4.9051844 9.3048468 + 3450 4.6741698 4.6317669 9.4965959 + 3500 4.8634066 4.9618835 8.926419 + 3550 4.7096981 4.4196734 9.5607265 + 3600 5.1871839 5.3427606 9.9467134 + 3650 5.7619975 5.2486309 10.359674 + 3700 5.2563068 5.4591612 10.360825 + 3750 5.2492743 5.4861677 9.7648858 + 3800 5.0335744 5.2240642 9.6668438 + 3850 5.1003253 5.0865548 11.111281 + 3900 5.2978019 5.2126205 10.581896 + 3950 5.0067291 5.2645911 10.750446 + 4000 4.6513682 4.7407991 9.3959165 + 4050 4.1903728 4.4021987 8.8451881 + 4100 5.0089655 4.4961608 9.7363416 + 4150 5.1557684 5.6110293 10.804015 + 4200 5.2607824 5.3663361 10.663617 + 4250 5.0134036 5.1164765 9.3320261 + 4300 4.2919496 4.6118896 9.2176556 + 4350 4.9118467 4.9766595 9.8989104 + 4400 5.7694762 5.2410849 10.660891 + 4450 5.3793656 5.4714178 10.784611 + 4500 5.187077 5.0952514 9.6404449 + 4550 4.9522826 4.5959954 10.30975 + 4600 4.9512246 5.0305627 10.295169 + 4650 5.8017637 5.3485687 10.411051 + 4700 5.2499784 4.8217382 10.077816 + 4750 4.9961796 4.9148313 9.4660475 + 4800 4.8958835 4.6546838 9.1730325 + 4850 4.7408482 5.1862514 9.9399226 + 4900 4.999383 4.9513486 9.5506941 + 4950 5.0375134 4.63474 10.325618 + 5000 5.0274884 5.391675 9.592851 + 5050 5.3817822 5.5141892 11.43286 + 5100 5.533224 5.1489534 10.56325 + 5150 4.4884587 4.8979144 9.7439562 + 5200 4.7352575 4.2854079 8.8328248 + 5250 4.6347427 4.7579757 9.5316726 + 5300 4.9765192 5.1378784 9.7376039 + 5350 5.1899675 4.9469798 10.699202 + 5400 5.0178189 5.47536 9.707559 + 5450 4.9537295 5.1651951 9.7430567 + 5500 4.8448459 4.6800231 9.297621 + 5550 5.1703386 4.865903 10.090954 + 5600 5.6293349 5.4332687 10.047955 + 5650 5.2729245 6.180173 10.259202 + 5700 5.1034054 5.2082315 10.031079 + 5750 5.0982009 5.0158875 10.3517 + 5800 4.8139573 4.8454398 10.001093 + 5850 5.3237843 4.9860148 10.493724 + 5900 4.421652 4.7147453 10.30137 + 5950 5.3475173 4.8489279 9.7495241 + 6000 5.013939 4.796874 9.7433063 + 6050 5.1111778 5.2773346 10.245638 + 6100 5.1484609 5.2230939 9.9800589 + 6150 5.0101213 5.0702323 9.7021038 + 6200 4.5881964 5.2635287 9.3903355 + 6250 5.5340791 5.5956851 10.809705 + 6300 5.3121762 5.3679934 9.4683653 + 6350 5.072589 5.0111289 10.494452 + 6400 5.3134876 5.3779245 11.439347 + 6450 4.9930408 5.3215491 10.287925 + 6500 4.6925854 4.4527123 9.3141266 + 6550 4.5127115 4.5276223 9.2970101 + 6600 4.6857945 5.0039986 9.8782575 + 6650 5.4210348 4.6775837 10.404812 + 6700 5.416291 5.1705872 10.935776 + 6750 5.2396825 5.0306589 10.14922 + 6800 5.3579349 4.9442072 10.510841 + 6850 4.8287972 4.4930847 9.4697502 + 6900 4.9688784 4.5977364 10.004321 + 6950 4.7853293 4.5578984 9.0727469 + 7000 5.0589506 4.9662362 11.04237 + 7050 5.2657677 5.3989373 10.712811 + 7100 5.5373555 5.6700228 10.099215 + 7150 4.7085526 4.4207863 9.417028 + 7200 4.7480934 4.8575585 9.970864 + 7250 5.2732588 5.211703 9.8573725 + 7300 5.0152654 5.5514349 11.104278 + 7350 4.9255785 5.3533123 10.69476 + 7400 5.1041241 5.0597338 9.5918592 + 7450 4.7333067 4.584844 10.820426 + 7500 4.9157751 5.0274623 10.706391 + 7550 4.8231717 5.2251684 9.7721097 + 7600 4.5115685 4.6809903 9.1230191 + 7650 4.76928 5.0869557 9.2881957 + 7700 5.1014383 5.4733369 9.9024386 + 7750 5.7812792 5.6404429 10.895814 + 7800 5.451651 5.4137204 10.471661 + 7850 4.7982757 5.2043999 10.046712 + 7900 4.4490306 4.546108 8.3934233 + 7950 4.3147055 4.489834 8.8833017 + 8000 5.0558378 5.1022203 11.21385 + 8050 6.0715673 5.9289687 12.007167 + 8100 5.4463621 5.8686057 9.7475724 + 8150 4.6295786 4.5658519 8.9353979 + 8200 4.4109788 4.4122705 8.8574801 + 8250 4.9903375 5.2807872 10.024069 + 8300 5.2930602 5.7480682 10.33242 + 8350 5.6166755 5.3279586 10.761278 + 8400 5.2344331 5.3991078 10.261601 + 8450 4.9395736 4.8421048 10.544976 + 8500 4.8692729 4.4538669 10.38133 + 8550 4.7746965 4.5959252 10.413873 + 8600 4.4344376 4.9176179 9.0368016 + 8650 5.0230802 4.7795825 8.5121429 + 8700 4.9279145 4.8844196 10.145405 + 8750 5.343116 5.7462499 11.191805 + 8800 5.4073851 5.1952022 9.6534892 + 8850 5.6085471 5.1332845 10.28282 + 8900 4.9077946 5.1446696 9.236557 + 8950 4.9416647 5.2071136 10.106251 + 9000 5.4201564 5.3733264 11.081109 + 9050 5.9648951 5.5501112 12.621681 + 9100 4.8947991 5.2187898 10.470022 + 9150 4.48197 4.1036268 8.4201904 + 9200 4.3946543 4.3973715 8.5340163 + 9250 5.3021965 5.2717867 9.2560849 + 9300 5.1768568 5.8272523 10.232503 + 9350 5.7291082 5.7641611 11.622836 + 9400 5.5971415 6.0957826 11.948662 + 9450 4.6317008 4.8550521 9.7699372 + 9500 4.3364192 4.4197985 8.8085022 + 9550 4.4961662 4.5930997 9.6064493 + 9600 4.901858 5.3789866 10.044551 + 9650 5.2916208 4.9071387 9.9083075 + 9700 4.8995154 4.78658 9.3871144 + 9750 5.5045136 5.3070515 10.969147 + 9800 5.2729372 6.0714054 11.027892 + 9850 4.8794625 5.2788176 10.100819 + 9900 4.6173961 4.6918339 9.2090718 + 9950 4.7478539 4.6911854 8.6831286 + 10000 4.9331146 5.3771408 11.489778 +Loop time of 2.62782 on 4 procs for 10000 steps with 500 atoms + +Performance: 1643945.149 tau/day, 3805.429 timesteps/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.29968 | 0.30667 | 0.31341 | 1.2 | 11.67 +Neigh | 1.0173 | 1.0395 | 1.0668 | 2.1 | 39.56 +Comm | 0.55804 | 0.59161 | 0.62132 | 3.5 | 22.51 +Output | 0.0028653 | 0.0035743 | 0.0056112 | 2.0 | 0.14 +Modify | 0.5692 | 0.5732 | 0.57625 | 0.4 | 21.81 +Other | | 0.1132 | | | 4.31 + +Nlocal: 125 ave 130 max 121 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Nghost: 452.25 ave 455 max 449 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 837 ave 882 max 804 min +Histogram: 2 0 0 0 0 0 1 0 0 1 + +Total # of neighbors = 3348 +Ave neighs/atom = 6.696 +Neighbor list builds = 4598 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/USER/uef/nvt_uniaxial/data.wca b/examples/USER/uef/nvt_uniaxial/data.wca new file mode 100644 index 0000000000..889ba4d2f2 --- /dev/null +++ b/examples/USER/uef/nvt_uniaxial/data.wca @@ -0,0 +1,1022 @@ +LAMMPS data file via write_data, version 14 May 2016, timestep = 400000 + +500 atoms +1 atom types + +0.0000000000000000e+00 8.3979809569125372e+00 xlo xhi +0.0000000000000000e+00 8.3979809569125372e+00 ylo yhi +0.0000000000000000e+00 8.3979809569125372e+00 zlo zhi + +Masses + +1 1 + +Pair Coeffs # lj/cut + +1 1 1 + +Atoms # atomic + +7 1 2.4137737201272674e-01 2.0017433398687118e-01 3.6157393311703534e-02 2 1 2 +398 1 1.6739594898193126e+00 3.0313452824803544e-01 5.7986723161362197e-01 -3 0 1 +173 1 6.1370793327804556e+00 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4.2843373407529362e-01 -8.1372583759538197e-01 +411 -7.0187880935114388e-01 -8.8403807864596529e-01 3.6139298123719504e-01 +396 -6.1324863673452068e-01 -5.8579142070009704e-01 -1.6980414017487730e+00 +424 -1.4405372913769463e+00 -1.2161267905238037e-01 -7.1275775203655271e-03 +66 -2.2455608800065441e-01 -5.5194985983545303e-02 -2.9031971555487707e-01 +371 2.8693892522161785e-01 -1.3942754264578394e-01 4.1638095135795372e-01 +186 -2.5542578648985415e-01 -2.7435394726950046e-01 1.6931522427410683e+00 +413 5.6007135922818607e-01 1.2189064363493711e-01 -7.5271223366515216e-01 diff --git a/examples/USER/uef/nvt_uniaxial/in.nvt_uniaxial b/examples/USER/uef/nvt_uniaxial/in.nvt_uniaxial new file mode 100644 index 0000000000..613f46935c --- /dev/null +++ b/examples/USER/uef/nvt_uniaxial/in.nvt_uniaxial @@ -0,0 +1,28 @@ +# uniaxial NVT deformation of WCA fluid + +units lj +atom_style atomic + + +pair_style lj/cut 1.122562 +read_data data.wca +pair_coeff 1 1 1.0 1.0 +pair_modify shift yes + +neighbor 0.5 bin +neigh_modify delay 0 + +change_box all triclinic + +fix 1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5 + +fix 2 all momentum 100 linear 1 1 1 + +#dump 1 all atom 25 dump.lammpstrj + +#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs + +thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] + +thermo 50 +run 10000 diff --git a/examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.1 b/examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.1 new file mode 100644 index 0000000000..1d6530ff46 --- /dev/null +++ b/examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.1 @@ -0,0 +1,273 @@ +LAMMPS (30 Jul 2016) +# uniaxial NVT deformation of WCA fluid + +units lj +atom_style atomic + + +pair_style lj/cut 1.122562 +read_data data.wca + orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities +pair_coeff 1 1 1.0 1.0 +pair_modify shift yes + +neighbor 0.5 bin +neigh_modify delay 0 + +change_box all triclinic + triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) + +fix 1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5 + +fix 2 all momentum 100 linear 1 1 1 + +#dump 1 all atom 25 dump.lammpstrj + +#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs + +thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] + +thermo 50 +run 10000 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.62256 + ghost atom cutoff = 1.62256 + binsize = 0.811281 -> bins = 11 11 11 +Memory usage per processor = 2.40217 Mbytes +Step 1_press[ 1_press[ 1_press[ + 0 6.3937851 7.0436438 6.4461087 + 50 10.369902 10.999889 6.5437384 + 100 12.411384 13.145871 7.8892802 + 150 12.88182 12.114068 7.5155182 + 200 10.375571 10.979773 6.5624056 + 250 10.158901 10.251273 5.4525068 + 300 10.011314 9.8371382 5.4031393 + 350 9.4890008 9.7992108 5.054963 + 400 9.1715116 9.2647886 4.9600208 + 450 9.8495961 9.3353483 4.986786 + 500 9.5903809 8.576173 4.8252116 + 550 8.8057509 9.7152078 4.9089022 + 600 8.9743682 10.031277 4.8924072 + 650 10.233852 9.3059527 5.1977058 + 700 9.2361906 9.6439971 5.0923763 + 750 10.449751 9.5911465 5.2548714 + 800 9.8366857 9.9873885 4.9456956 + 850 10.266351 9.9620134 5.0602713 + 900 9.6325813 9.3910946 5.1466624 + 950 9.1911919 9.1519006 4.8275345 + 1000 9.2871712 9.8508501 5.2674099 + 1050 9.7052035 10.291793 5.160359 + 1100 9.9425552 10.361827 5.5520484 + 1150 10.377563 10.26588 5.5997436 + 1200 9.6368269 10.354413 5.4137873 + 1250 9.2071055 9.1706334 4.9800411 + 1300 9.7140516 8.7257777 4.8536943 + 1350 10.145983 9.8247797 4.8921813 + 1400 9.1998975 9.6935675 5.2269871 + 1450 9.4838136 8.9035726 4.6867121 + 1500 9.066389 9.811658 4.8875316 + 1550 10.007083 9.8946118 5.204609 + 1600 9.722137 9.9291588 5.326712 + 1650 9.7424614 9.6995966 5.3577819 + 1700 9.7185135 9.5922931 5.385856 + 1750 9.6368481 8.1414594 5.0046079 + 1800 9.8065782 9.6798036 4.92473 + 1850 9.0463737 10.024205 5.6495695 + 1900 9.0774484 10.527582 5.0363426 + 1950 9.1691461 10.049703 4.8517514 + 2000 9.7619602 10.049532 5.2088038 + 2050 9.9203348 9.8056395 5.7699852 + 2100 9.1455665 9.5864018 5.1410542 + 2150 8.8501135 9.7917307 5.141824 + 2200 9.1433685 9.8168548 5.1742441 + 2250 9.3248968 10.454532 5.5456356 + 2300 10.210505 9.361499 5.0935226 + 2350 9.5041186 9.598986 5.2451005 + 2400 8.968896 9.2811921 4.7799868 + 2450 9.8201159 10.133892 4.9981817 + 2500 9.4421084 9.7875766 5.4124809 + 2550 9.6410643 9.9148309 5.0603288 + 2600 9.3810676 9.5346849 5.3233836 + 2650 9.2340337 8.7233538 5.0361302 + 2700 9.405597 9.7848488 4.7537042 + 2750 9.9447412 9.2366502 4.9736459 + 2800 10.189443 9.452684 5.624362 + 2850 9.6680124 9.0941543 5.0101469 + 2900 8.4350889 9.1595018 4.7706866 + 2950 9.0056117 9.3498593 4.7655963 + 3000 9.4795416 9.7400747 5.4705868 + 3050 9.6605264 9.4558374 5.1240166 + 3100 9.681451 9.7966554 5.3174458 + 3150 9.7887528 9.7371194 4.9349103 + 3200 9.9720054 9.5592538 5.2306417 + 3250 10.185023 9.9436037 5.4127312 + 3300 9.9670676 9.6069307 5.026261 + 3350 9.0090411 9.5975249 4.8881019 + 3400 9.6535707 9.748683 4.9933873 + 3450 9.7774977 9.7570511 4.8512619 + 3500 9.7250053 10.36386 5.4057249 + 3550 9.567788 9.773413 5.3936671 + 3600 9.2094148 9.0211247 5.2328675 + 3650 9.3512098 9.73407 4.576624 + 3700 9.159074 9.2611591 5.2996448 + 3750 9.4772798 8.9792211 5.1007079 + 3800 9.3898357 9.1150609 5.2126508 + 3850 9.2466312 9.1460651 4.867472 + 3900 9.9316993 9.3061137 5.1219265 + 3950 9.2550913 9.780254 5.371885 + 4000 10.005356 9.7328972 5.2535791 + 4050 9.5228242 9.5134113 5.4181393 + 4100 9.576808 10.082425 5.1272491 + 4150 10.20265 9.6667058 5.529118 + 4200 9.9443671 10.09427 5.6163734 + 4250 9.4956875 9.9462818 5.0820085 + 4300 10.350144 10.003702 5.1621505 + 4350 10.119486 9.8691507 5.4913457 + 4400 9.4991604 10.516185 5.2512264 + 4450 9.0812854 9.2835603 5.1695714 + 4500 9.7538478 8.5298834 4.5954607 + 4550 9.8920394 9.3581299 5.202587 + 4600 9.2694921 9.3338291 5.201958 + 4650 10.925818 9.5062049 4.8694531 + 4700 11.020014 10.130224 5.582409 + 4750 9.5005142 9.3571561 5.456739 + 4800 9.6670147 9.6628702 5.0451252 + 4850 9.134147 9.1308788 4.7950594 + 4900 9.7466206 8.6171443 4.8716275 + 4950 9.0397505 9.1996036 5.2010502 + 5000 9.6898652 9.8914655 5.3959279 + 5050 10.06771 9.7523891 5.3690408 + 5100 10.000963 9.6279379 5.4077384 + 5150 9.8686159 10.179702 5.0686824 + 5200 9.8866247 9.725152 5.4350049 + 5250 9.2068346 10.214424 5.3187713 + 5300 9.713992 9.8069045 5.496359 + 5350 9.423852 9.364085 5.2144606 + 5400 9.4350241 9.5584633 5.0339001 + 5450 10.555124 10.784922 5.1938072 + 5500 9.4147344 10.33187 5.4360602 + 5550 9.8514653 9.6575827 5.4959779 + 5600 9.3138107 9.6592624 4.941387 + 5650 9.1224809 8.7112257 5.0435936 + 5700 8.8289158 10.749686 4.8916132 + 5750 9.7200279 10.030606 5.2033161 + 5800 9.8439873 9.6289015 5.5131934 + 5850 9.6257294 9.4128988 4.9196038 + 5900 9.7490214 9.5776313 5.0301815 + 5950 9.1430855 10.108944 5.1406243 + 6000 9.3358644 9.5633737 4.9787073 + 6050 9.4432774 8.9464304 5.1466052 + 6100 8.8878373 9.5048946 4.9190238 + 6150 9.6451898 9.2419823 5.0159841 + 6200 9.5042173 8.9414307 5.2634247 + 6250 9.0896505 9.7230651 5.3340322 + 6300 8.8100599 8.8781352 5.4117914 + 6350 9.3104601 9.0233294 5.3136432 + 6400 9.368101 9.6387362 4.7833216 + 6450 10.334343 9.8384149 5.3606204 + 6500 9.8824036 10.022627 6.0857086 + 6550 9.7034443 10.026765 5.17604 + 6600 9.3757845 9.899268 5.2301359 + 6650 10.540821 10.4343 5.5287065 + 6700 9.6317649 9.8923579 5.6045768 + 6750 9.5982772 10.07897 5.1221451 + 6800 10.239883 10.189967 5.3167447 + 6850 10.017271 9.7680902 5.229621 + 6900 9.6200416 10.129301 5.1998759 + 6950 9.0361417 8.923798 5.1652612 + 7000 9.3153521 9.063054 4.6860773 + 7050 8.6434091 9.0363436 4.7811975 + 7100 9.4955395 9.3830541 5.022538 + 7150 9.3392402 9.1847119 5.1544622 + 7200 9.4676321 9.8370036 4.8854442 + 7250 9.5115882 10.350324 4.9780525 + 7300 9.6025583 9.6247917 5.473794 + 7350 9.8919524 10.049446 4.9816931 + 7400 9.6814319 9.9410894 5.265078 + 7450 9.4130955 10.191436 5.2531256 + 7500 9.8114668 8.8461635 5.0562894 + 7550 10.321567 9.4730124 5.2043655 + 7600 9.5059024 9.8330367 5.0749721 + 7650 10.067084 10.606423 5.5598818 + 7700 10.896159 10.084281 5.5159718 + 7750 9.754306 10.162301 5.2475876 + 7800 9.7278145 9.801009 5.0685504 + 7850 9.8639905 10.323104 5.2458864 + 7900 9.7246799 9.1377357 5.1841319 + 7950 10.381792 9.6977533 5.0977386 + 8000 9.7265224 9.2999829 4.7925571 + 8050 9.5203288 9.3144956 4.7539211 + 8100 9.6900973 9.6614063 5.304712 + 8150 9.713677 9.9154149 4.8178575 + 8200 9.4733597 9.8948632 5.036112 + 8250 9.7783036 9.9554334 5.3355682 + 8300 9.4034783 9.9156801 5.5539279 + 8350 9.2984025 9.2013949 5.0753991 + 8400 9.9299078 9.6166801 5.115776 + 8450 9.526737 9.3312125 4.7800587 + 8500 9.581956 10.065906 4.9756092 + 8550 9.2767953 9.326006 5.3024978 + 8600 9.799968 8.4660845 5.0199109 + 8650 9.8985354 10.127852 4.9098064 + 8700 8.7952691 10.521133 5.6840528 + 8750 9.8299997 9.5588553 5.3085734 + 8800 9.0811776 9.5704532 5.1684993 + 8850 9.8303571 9.7618932 5.1251259 + 8900 9.9238794 9.9654863 5.2999683 + 8950 10.851304 9.9682289 5.4133763 + 9000 9.5523794 9.1890766 5.1469144 + 9050 9.7461948 8.9611236 4.9490826 + 9100 10.138917 9.6757567 5.0473544 + 9150 9.4869835 9.4786575 5.0142464 + 9200 10.263518 10.079135 5.1493398 + 9250 9.8691684 9.0908275 5.3221203 + 9300 9.8586707 9.4177643 5.1525265 + 9350 9.3375816 9.9167208 5.4846207 + 9400 9.5603903 9.4813199 4.6237495 + 9450 10.30892 9.5217736 5.6163214 + 9500 9.327949 9.9831649 4.8923915 + 9550 9.8421656 9.3202702 5.3352046 + 9600 8.8543704 9.4556702 4.6430041 + 9650 10.103399 9.2161072 4.8658062 + 9700 9.507811 9.9647378 5.227369 + 9750 9.4988096 8.9942893 5.2491418 + 9800 9.8007958 9.234452 5.1740203 + 9850 9.6029685 10.076042 5.023107 + 9900 9.4035691 10.13782 5.2775777 + 9950 9.6517135 10.355994 5.3035779 + 10000 9.9157616 9.7741952 5.5269431 +Loop time of 4.303 on 1 procs for 10000 steps with 500 atoms + +Performance: 1003950.961 tau/day, 2323.961 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.69667 | 0.69667 | 0.69667 | 0.0 | 16.19 +Neigh | 2.699 | 2.699 | 2.699 | 0.0 | 62.72 +Comm | 0.30701 | 0.30701 | 0.30701 | 0.0 | 7.13 +Output | 0.003968 | 0.003968 | 0.003968 | 0.0 | 0.09 +Modify | 0.49374 | 0.49374 | 0.49374 | 0.0 | 11.47 +Other | | 0.1026 | | | 2.38 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 908 ave 908 max 908 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3489 ave 3489 max 3489 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3489 +Ave neighs/atom = 6.978 +Neighbor list builds = 4567 +Dangerous builds = 0 +Total wall time: 0:00:04 diff --git a/examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.4 b/examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.4 new file mode 100644 index 0000000000..f977bf4e7d --- /dev/null +++ b/examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.4 @@ -0,0 +1,273 @@ +LAMMPS (30 Jul 2016) +# uniaxial NVT deformation of WCA fluid + +units lj +atom_style atomic + + +pair_style lj/cut 1.122562 +read_data data.wca + orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities +pair_coeff 1 1 1.0 1.0 +pair_modify shift yes + +neighbor 0.5 bin +neigh_modify delay 0 + +change_box all triclinic + triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) + +fix 1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5 + +fix 2 all momentum 100 linear 1 1 1 + +#dump 1 all atom 25 dump.lammpstrj + +#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs + +thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] + +thermo 50 +run 10000 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.62256 + ghost atom cutoff = 1.62256 + binsize = 0.811281 -> bins = 11 11 11 +Memory usage per processor = 2.38201 Mbytes +Step 1_press[ 1_press[ 1_press[ + 0 6.3937851 7.0436438 6.4461087 + 50 10.369902 10.999889 6.5437384 + 100 12.411384 13.145871 7.8892802 + 150 12.88182 12.114068 7.5155182 + 200 10.375571 10.979773 6.5624056 + 250 10.158901 10.251273 5.4525068 + 300 10.011314 9.8371382 5.4031393 + 350 9.4890008 9.7992108 5.054963 + 400 9.1715116 9.2647886 4.9600208 + 450 9.8495961 9.3353483 4.986786 + 500 9.5903809 8.576173 4.8252116 + 550 8.8057509 9.7152078 4.9089022 + 600 8.9743682 10.031277 4.8924072 + 650 10.233852 9.3059527 5.1977058 + 700 9.2361906 9.6439971 5.0923762 + 750 10.449751 9.5911465 5.2548714 + 800 9.8366858 9.9873885 4.9456956 + 850 10.266351 9.9620134 5.0602713 + 900 9.6325811 9.3910947 5.1466627 + 950 9.1911905 9.1518997 4.8275335 + 1000 9.2871725 9.8508561 5.2674079 + 1050 9.7052018 10.291782 5.1603606 + 1100 9.942582 10.361849 5.5520591 + 1150 10.37757 10.265893 5.5997259 + 1200 9.6367107 10.354442 5.4138733 + 1250 9.2075329 9.1705 4.9806587 + 1300 9.7125232 8.724748 4.852827 + 1350 10.146185 9.8320894 4.8958299 + 1400 9.1958247 9.7053023 5.2334931 + 1450 9.4656613 8.9011194 4.7069541 + 1500 9.0964228 9.8379154 4.8889701 + 1550 10.074953 9.8121208 5.1614034 + 1600 10.14322 9.7113028 5.0901612 + 1650 9.9377801 9.8831912 5.2226793 + 1700 9.4144883 8.5248477 4.9447402 + 1750 9.0729219 9.612432 5.1999941 + 1800 10.067363 9.8211216 5.1464764 + 1850 9.3044429 8.9752352 5.0515339 + 1900 9.4123739 9.1810527 5.3356061 + 1950 9.3009721 10.013851 4.9527398 + 2000 9.7741829 10.11286 5.3818321 + 2050 9.6991106 9.7815812 5.1979016 + 2100 9.2977435 9.4310005 5.0893893 + 2150 10.325992 10.388415 4.9253076 + 2200 10.193251 10.389764 5.4164579 + 2250 9.9386988 9.63934 5.1685251 + 2300 9.3128664 10.496199 5.423297 + 2350 8.692096 9.761347 5.1356802 + 2400 9.4532892 9.2946894 5.3127538 + 2450 9.026436 8.8042728 4.9305279 + 2500 8.9458518 9.6338731 5.1530972 + 2550 8.9457961 9.7730997 5.1588 + 2600 9.4313048 9.0489105 4.9937356 + 2650 9.1625701 10.03039 4.9384831 + 2700 10.135274 9.9106295 5.1582637 + 2750 9.7419819 9.7329998 5.4813308 + 2800 9.6793568 10.137218 4.9126985 + 2850 9.8286116 9.8283148 5.2372177 + 2900 9.2766894 9.5302835 5.1206658 + 2950 9.6537203 9.8713609 5.2640351 + 3000 9.704446 10.360629 5.2470236 + 3050 9.289114 10.210593 4.9955164 + 3100 9.5854695 9.0377602 5.0387963 + 3150 9.4489179 9.0145734 4.9089788 + 3200 8.9221328 8.8805863 4.7910012 + 3250 8.9268792 8.6855592 4.7798689 + 3300 9.5280088 9.6859376 5.1021255 + 3350 9.7469167 9.7039449 5.3654161 + 3400 10.163823 10.247303 5.3206912 + 3450 10.328168 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5.1395845 + 4850 8.8662041 9.4757304 5.1729905 + 4900 9.6230855 10.239009 5.1382048 + 4950 10.401327 9.5494971 5.2688637 + 5000 10.433047 9.9017863 5.4626886 + 5050 10.318188 9.2998964 5.4707543 + 5100 9.6958274 9.206341 5.0269859 + 5150 9.5477552 10.099142 5.3760873 + 5200 9.4904189 9.4403777 5.1638292 + 5250 9.8421539 8.7828543 4.8612713 + 5300 9.7354196 9.357113 4.9059656 + 5350 9.9183987 9.4337973 5.2986167 + 5400 10.045743 9.8399757 5.0930923 + 5450 9.6414177 10.169944 5.3868716 + 5500 10.035214 9.5316451 4.912222 + 5550 9.16334 9.3853532 5.2319683 + 5600 9.5075535 9.2548959 5.4425531 + 5650 9.3854437 9.0700172 4.9845383 + 5700 9.1868937 9.3061525 4.9155762 + 5750 9.4785528 9.8271693 4.9974045 + 5800 9.7809419 10.070618 5.3699816 + 5850 10.791132 10.572676 5.3816834 + 5900 10.091884 10.036391 5.7604455 + 5950 9.4492785 8.9938163 4.9812227 + 6000 9.2296463 10.334517 5.6374553 + 6050 9.9339781 9.1097471 4.6847041 + 6100 10.369857 9.261491 5.3354256 + 6150 9.9444024 9.5330721 5.2413981 + 6200 9.1507255 9.2108005 4.7010871 + 6250 9.6093995 9.2275894 4.8659261 + 6300 9.0300283 9.149341 4.9305141 + 6350 9.6718904 9.5721387 4.9560051 + 6400 9.615362 10.030978 4.8786582 + 6450 10.343763 10.184481 5.2027613 + 6500 9.3452563 9.7249417 5.2318842 + 6550 9.9489414 10.373436 4.9258407 + 6600 10.083741 10.87974 5.3665699 + 6650 9.431476 9.7944015 5.4214407 + 6700 9.3430129 10.032417 4.8538936 + 6750 10.253341 9.5667637 5.3838115 + 6800 8.9695591 9.888476 4.7973343 + 6850 9.6952765 9.3339082 4.8432603 + 6900 9.1038139 9.6295207 4.8572214 + 6950 9.5374663 9.0498856 5.2316356 + 7000 8.6844415 9.1416318 4.9513449 + 7050 9.6271147 8.8341922 5.135948 + 7100 9.3889214 9.6771129 5.1106028 + 7150 9.4697432 9.9959141 4.8762717 + 7200 9.9545962 9.5556848 5.2760968 + 7250 10.153728 10.396722 5.4066282 + 7300 9.5633599 9.8262997 5.5238788 + 7350 10.476059 9.8526241 4.9928222 + 7400 9.5848947 9.389115 5.1177333 + 7450 9.3917853 9.8395056 5.5201002 + 7500 9.2406374 9.4598141 4.9336365 + 7550 9.1325284 9.0585 5.007436 + 7600 9.5045307 9.5164648 4.8310378 + 7650 9.5165952 9.5154581 5.3199138 + 7700 9.1167042 9.3283907 4.9548988 + 7750 9.5408306 10.191558 5.1889476 + 7800 9.2362359 9.5066276 5.4139251 + 7850 9.9533215 9.3418618 5.0073354 + 7900 9.063471 9.2389687 5.1529568 + 7950 9.6887619 9.3363144 5.0264365 + 8000 10.244559 10.352116 5.3898068 + 8050 10.522656 9.7844249 5.648648 + 8100 10.456047 10.108097 5.234203 + 8150 9.0497599 10.3333 5.5526068 + 8200 9.1341912 9.7046196 4.7491692 + 8250 9.3297032 9.2513325 4.9471519 + 8300 9.9385635 9.8432553 4.9102209 + 8350 9.506086 9.3628428 5.4489526 + 8400 9.7575572 9.6628477 4.7835143 + 8450 9.4234184 9.6901535 5.2506704 + 8500 9.1019018 9.4713605 4.9996292 + 8550 8.9668254 9.2297952 4.9015639 + 8600 10.000082 9.852912 5.1235791 + 8650 9.6677771 9.8825377 5.0888713 + 8700 9.5220305 9.6140025 5.2621374 + 8750 9.769165 9.1639605 4.942283 + 8800 10.214712 9.0544214 5.0977658 + 8850 10.050644 8.9450446 4.876467 + 8900 9.7066878 9.8028705 5.1098917 + 8950 9.8322209 9.5247394 5.1258681 + 9000 10.116755 9.9220422 5.2801505 + 9050 9.671068 9.448618 5.1789641 + 9100 8.6872235 9.8346401 4.8940421 + 9150 9.8181714 9.652061 4.9136383 + 9200 9.5400873 9.9027439 5.3147415 + 9250 9.2344784 9.9272383 5.397571 + 9300 9.0207063 9.2498921 5.0643988 + 9350 10.648665 9.0509298 5.0354353 + 9400 9.7266263 9.5319347 5.4323366 + 9450 9.5044169 9.7968623 5.2079039 + 9500 9.0459316 9.6916313 5.1584987 + 9550 9.1265901 10.045493 4.9476229 + 9600 9.896449 9.509792 5.5305989 + 9650 9.2957435 9.4288068 5.1885785 + 9700 9.6000499 8.7187335 5.0900953 + 9750 9.5997652 9.4810899 4.8707106 + 9800 9.2198937 9.7067006 5.4461186 + 9850 9.8794169 10.051937 5.0361319 + 9900 9.9783069 9.9785092 5.2066807 + 9950 9.0880268 9.5659803 5.3678011 + 10000 9.6972182 9.9076171 5.1538951 +Loop time of 2.23728 on 4 procs for 10000 steps with 500 atoms + +Performance: 1930919.704 tau/day, 4469.722 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.26111 | 0.26444 | 0.26854 | 0.5 | 11.82 +Neigh | 1.0268 | 1.037 | 1.0467 | 0.7 | 46.35 +Comm | 0.5321 | 0.55022 | 0.56515 | 1.6 | 24.59 +Output | 0.003746 | 0.0045477 | 0.006809 | 1.9 | 0.20 +Modify | 0.26509 | 0.26827 | 0.27182 | 0.5 | 11.99 +Other | | 0.1128 | | | 5.04 + +Nlocal: 125 ave 128 max 123 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Nghost: 468.25 ave 470 max 467 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 869.75 ave 895 max 843 min +Histogram: 1 0 0 0 1 0 1 0 0 1 + +Total # of neighbors = 3479 +Ave neighs/atom = 6.958 +Neighbor list builds = 4555 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/src/Makefile b/src/Makefile index 243ac869e9..e0f0db77fe 100644 --- a/src/Makefile +++ b/src/Makefile @@ -63,7 +63,7 @@ PACKUSER = user-atc user-awpmd user-cgdna user-cgsdk user-colvars \ user-mgpt user-misc user-molfile \ user-netcdf user-omp user-phonon user-qmmm user-qtb \ user-quip user-reaxc user-smd user-smtbq user-sph user-tally \ - user-vtk + user-uef user-vtk PACKLIB = compress gpu kim kokkos latte meam mpiio mscg poems \ python reax voronoi \ diff --git a/src/USER-UEF/compute_pressure_uef.cpp b/src/USER-UEF/compute_pressure_uef.cpp new file mode 100644 index 0000000000..e9bbdf0cf4 --- /dev/null +++ b/src/USER-UEF/compute_pressure_uef.cpp @@ -0,0 +1,198 @@ +/* ---------------------------------------------------------------------- + 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. + + Contributing author: David Nicholson (MIT) +------------------------------------------------------------------------- */ + +#include "mpi.h" +#include "string.h" +#include "stdlib.h" +#include "compute_pressure_uef.h" +#include "fix_nh_uef.h" +#include "update.h" +#include "domain.h" +#include "modify.h" +#include "fix.h" +#include "force.h" +#include "pair.h" +#include "bond.h" +#include "angle.h" +#include "dihedral.h" +#include "improper.h" +#include "kspace.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- + * Default values for the ext flags + * ----------------------------------------------------------------------*/ +ComputePressureUef::ComputePressureUef(LAMMPS *lmp, int narg, char **arg) : + ComputePressure(lmp, narg, arg) + { + ext_flags[0] = true; + ext_flags[1] = true; + ext_flags[2] = true; + in_fix=false; + } + +/* ---------------------------------------------------------------------- + * Check for the uef fix + * ----------------------------------------------------------------------*/ +void ComputePressureUef::init() +{ + ComputePressure::init(); + // check to make sure the other uef fix is on + // borrowed from Pieter's nvt/sllod code + int i=0; + for (i=0; infix; i++) + { + if (strcmp(modify->fix[i]->style,"nvt/uef")==0) + break; + if (strcmp(modify->fix[i]->style,"npt/uef")==0) + break; + } + if (i==modify->nfix) + error->all(FLERR,"Can't use compute pressure/uef without defining a fix nvt/npt/uef"); + ifix_uef=i; + ((FixNHUef*) modify->fix[ifix_uef])->get_ext_flags(ext_flags); + + if (strcmp(temperature->style,"temp/uef") != 0) + error->warning(FLERR,"The temperature used in compute pressure/ued is not of style temp/uef"); +} + +/* ---------------------------------------------------------------------- + * Compute pressure in the directions i corresponding to ext_flag[i]=true + * ----------------------------------------------------------------------*/ +double ComputePressureUef::compute_scalar() +{ + + temperature->compute_scalar(); +// if all pressures are external the scalar is found as normal + if (ext_flags[0] && ext_flags[1] && ext_flags[2]) + return ComputePressure::compute_scalar(); + +// otherwise compute the full tensor and average desired components + compute_vector(); + addstep(update->ntimestep+1); + + int k =0; + scalar = 0; + if (ext_flags[0]) + { + scalar += vector[0]; + k++; + } + if (ext_flags[1]) + { + scalar += vector[1]; + k++; + } + if (ext_flags[2]) + { + scalar += vector[2]; + k++; + } + + scalar /= k; + return scalar; +} + +/* ---------------------------------------------------------------------- + Compute the pressure tensor in the rotated coordinate system +------------------------------------------------------------------------- */ +void ComputePressureUef::compute_vector() +{ + invoked_vector = update->ntimestep; + if (update->vflag_global != invoked_vector) + error->all(FLERR,"Virial was not tallied on needed timestep"); + + if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag) + error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for " + "tensor components with kspace_style msm"); + + // invoke temperature if it hasn't been already + + double *ke_tensor; + if (keflag) { + if (temperature->invoked_vector != update->ntimestep) + temperature->compute_vector(); + ke_tensor = temperature->vector; + } + + if (dimension == 3) { + inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd); + virial_compute(6,3); + if (in_fix) + virial_rot(virial,rot); + else + { + double r[3][3]; + ( (FixNHUef*) modify->fix[ifix_uef])->get_rot(r); + virial_rot(virial,r); + } + if (keflag) { + for (int i = 0; i < 6; i++) + vector[i] = (ke_tensor[i] + virial[i]) * inv_volume * nktv2p; + } else + for (int i = 0; i < 6; i++) + vector[i] = virial[i] * inv_volume * nktv2p; + } else { + inv_volume = 1.0 / (domain->xprd * domain->yprd); + virial_compute(4,2); + if (keflag) { + vector[0] = (ke_tensor[0] + virial[0]) * inv_volume * nktv2p; + vector[1] = (ke_tensor[1] + virial[1]) * inv_volume * nktv2p; + vector[3] = (ke_tensor[3] + virial[3]) * inv_volume * nktv2p; + vector[2] = vector[4] = vector[5] = 0.0; + } else { + vector[0] = virial[0] * inv_volume * nktv2p; + vector[1] = virial[1] * inv_volume * nktv2p; + vector[3] = virial[3] * inv_volume * nktv2p; + vector[2] = vector[4] = vector[5] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- + * get the current rotation matrix and store it +------------------------------------------------------------------------- */ +void ComputePressureUef::update_rot() +{ + ( (FixNHUef*) modify->fix[ifix_uef])->get_rot(rot); +} + +/* ---------------------------------------------------------------------- + Transform the pressure tensor to the rotated coordinate system + [P]rot = Q.[P].Q^t +------------------------------------------------------------------------- */ +void ComputePressureUef::virial_rot(double *x, const double r[3][3]) +{ + + double t[3][3]; + // [00 10 20 ] [ 0 3 4 ] [00 01 02 ] + // [01 11 21 ] [ 3 1 5 ] [10 11 12 ] + // [02 12 22 ] [ 4 5 2 ] [20 21 22 ] + for (int k = 0; k<3; ++k) + { + t[0][k] = x[0]*r[0][k] + x[3]*r[1][k] + x[4]*r[2][k]; + t[1][k] = x[3]*r[0][k] + x[1]*r[1][k] + x[5]*r[2][k]; + t[2][k] = x[4]*r[0][k] + x[5]*r[1][k] + x[2]*r[2][k]; + } + x[0] = r[0][0]*t[0][0] + r[1][0]*t[1][0] + r[2][0]*t[2][0]; + x[3] = r[0][0]*t[0][1] + r[1][0]*t[1][1] + r[2][0]*t[2][1]; + x[4] = r[0][0]*t[0][2] + r[1][0]*t[1][2] + r[2][0]*t[2][2]; + x[1] = r[0][1]*t[0][1] + r[1][1]*t[1][1] + r[2][1]*t[2][1]; + x[5] = r[0][1]*t[0][2] + r[1][1]*t[1][2] + r[2][1]*t[2][2]; + x[2] = r[0][2]*t[0][2] + r[1][2]*t[1][2] + r[2][2]*t[2][2]; +} + diff --git a/src/USER-UEF/compute_pressure_uef.h b/src/USER-UEF/compute_pressure_uef.h new file mode 100644 index 0000000000..2f591b64d8 --- /dev/null +++ b/src/USER-UEF/compute_pressure_uef.h @@ -0,0 +1,66 @@ +/* ---------------------------------------------------------------------- + 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. + + Contributing author: David Nicholson (MIT) +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(pressure/uef,ComputePressureUef) + +#else + +#ifndef LMP_COMPUTE_PRESSURE_UEF_H +#define LMP_COMPUTE_PRESSURE_UEF_H + +#include "compute_pressure.h" + +namespace LAMMPS_NS { + +class ComputePressureUef : public ComputePressure { + public: + ComputePressureUef(class LAMMPS *, int, char **); + virtual ~ComputePressureUef(){} + virtual void init(); + virtual void compute_vector(); + virtual double compute_scalar(); + void update_rot(); + bool in_fix; //true if this compute is used in fix/nvt/npt + + + protected: + bool ext_flags[3]; // true if used in average output pressure + void virial_rot(double*,const double[3][3]); + int ifix_uef; + double rot[3][3]; +}; + + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +This class inherits most of the warnings from ComputePressure. The +only additions are: + +E: Can't use compute pressure/uef without defining a fix nvt/npt/uef + +Self-explanatory. + +W: The temperature used in compute pressure/uef is not of style temp/uef + +Self-explanatory. + +*/ diff --git a/src/USER-UEF/compute_temp_uef.cpp b/src/USER-UEF/compute_temp_uef.cpp new file mode 100644 index 0000000000..8c8c9be293 --- /dev/null +++ b/src/USER-UEF/compute_temp_uef.cpp @@ -0,0 +1,110 @@ +/* ---------------------------------------------------------------------- + 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. + + Contributing author: David Nicholson (MIT) +------------------------------------------------------------------------- */ + +#include "string.h" +#include "stdlib.h" +#include "compute_temp_uef.h" +#include "fix_nh_uef.h" +#include "update.h" +#include "modify.h" +#include "fix.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- + * Base constructor initialized to use rotation matrix + * ----------------------------------------------------------------------*/ +ComputeTempUef::ComputeTempUef(LAMMPS *lmp, int narg, char **arg) : + ComputeTemp(lmp, narg, arg) +{ + rot_flag=true; +} + +/* ---------------------------------------------------------------------- + * Check for the uef fix + * ----------------------------------------------------------------------*/ +void ComputeTempUef::init() +{ + ComputeTemp::init(); + // check to make sure the other uef fix is on + // borrowed from Pieter's nvt/sllod code + int i=0; + for (i=0; infix; i++) + { + if (strcmp(modify->fix[i]->style,"nvt/uef")==0) + break; + if (strcmp(modify->fix[i]->style,"npt/uef")==0) + break; + } + if (i==modify->nfix) + error->all(FLERR,"Can't use compute temp/uef without defining a fix nvt/npt/uef"); + ifix_uef=i; +} + + +/* ---------------------------------------------------------------------- + Compute the ke tensor in the proper coordinate system +------------------------------------------------------------------------- */ +void ComputeTempUef::compute_vector() +{ + ComputeTemp::compute_vector(); + if (rot_flag) + { + double rot[3][3]; + ( (FixNHUef*) modify->fix[ifix_uef])->get_rot(rot); + virial_rot(vector,rot); + } + +} + +/* ---------------------------------------------------------------------- + * turn the rotation matrix on or off to properly account for the + * coordinate system of the velocities +------------------------------------------------------------------------- */ +void ComputeTempUef::yes_rot() +{ + rot_flag =true; +} +void ComputeTempUef::no_rot() +{ + rot_flag =false; +} + +/* ---------------------------------------------------------------------- + Transform the pressure tensor to the rotated coordinate system + [P]rot = Q.[P].Q^t +------------------------------------------------------------------------- */ +void ComputeTempUef::virial_rot(double *x, const double r[3][3]) +{ + + double t[3][3]; + // [00 10 20 ] [ 0 3 4 ] [00 01 02 ] + // [01 11 21 ] [ 3 1 5 ] [10 11 12 ] + // [02 12 22 ] [ 4 5 2 ] [20 21 22 ] + for (int k = 0; k<3; ++k) + { + t[0][k] = x[0]*r[0][k] + x[3]*r[1][k] + x[4]*r[2][k]; + t[1][k] = x[3]*r[0][k] + x[1]*r[1][k] + x[5]*r[2][k]; + t[2][k] = x[4]*r[0][k] + x[5]*r[1][k] + x[2]*r[2][k]; + } + x[0] = r[0][0]*t[0][0] + r[1][0]*t[1][0] + r[2][0]*t[2][0]; + x[3] = r[0][0]*t[0][1] + r[1][0]*t[1][1] + r[2][0]*t[2][1]; + x[4] = r[0][0]*t[0][2] + r[1][0]*t[1][2] + r[2][0]*t[2][2]; + x[1] = r[0][1]*t[0][1] + r[1][1]*t[1][1] + r[2][1]*t[2][1]; + x[5] = r[0][1]*t[0][2] + r[1][1]*t[1][2] + r[2][1]*t[2][2]; + x[2] = r[0][2]*t[0][2] + r[1][2]*t[1][2] + r[2][2]*t[2][2]; +} + diff --git a/src/USER-UEF/compute_temp_uef.h b/src/USER-UEF/compute_temp_uef.h new file mode 100644 index 0000000000..2e9dc901c0 --- /dev/null +++ b/src/USER-UEF/compute_temp_uef.h @@ -0,0 +1,60 @@ +/* ---------------------------------------------------------------------- + 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. + + Contributing author: David Nicholson (MIT) +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(temp/uef,ComputeTempUef) + +#else + +#ifndef LMP_COMPUTE_TEMP_UEF_H +#define LMP_COMPUTE_TEMP_UEF_H + +#include "compute_temp.h" + +namespace LAMMPS_NS { + +class ComputeTempUef : public ComputeTemp { + public: + ComputeTempUef(class LAMMPS *, int, char **); + virtual ~ComputeTempUef(){} + virtual void init(); + virtual void compute_vector(); + void yes_rot(); + void no_rot(); + + + protected: + bool rot_flag; + void virial_rot(double*,const double[3][3]); + int ifix_uef; +}; + + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +This class inherits most of the warnings from ComputePressure. The +only addition is: + +E: Can't use compute temp/uef without defining a fix nvt/npt/uef + +Self-explanatory. + +*/ diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/USER-UEF/dump_cfg_uef.cpp new file mode 100644 index 0000000000..2ee216934c --- /dev/null +++ b/src/USER-UEF/dump_cfg_uef.cpp @@ -0,0 +1,113 @@ +/* ---------------------------------------------------------------------- + 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. + + Contributing Author: David Nicholson (MIT) +------------------------------------------------------------------------- */ + + +#include +#include +#include +#include "dump_cfg.h" +#include "atom.h" +#include "domain.h" +#include "modify.h" +#include "compute.h" +#include "fix.h" +#include "error.h" +#include "dump_cfg_uef.h" +#include "fix_nh_uef.h" + +using namespace LAMMPS_NS; + +enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCustom + +#define UNWRAPEXPAND 10.0 +#define ONEFIELD 32 +#define DELTA 1048576 + +/* ---------------------------------------------------------------------- + * base method is mostly fine, just need to find the FixNHUef + * ----------------------------------------------------------------------*/ +void DumpCFGUef::init_style() +{ + DumpCFG::init_style(); + + // check to make sure the other uef fix is on + // borrowed from Pieter's nvt/sllod code + int i=0; + for (i=0; infix; i++) + { + if (strcmp(modify->fix[i]->style,"nvt/uef")==0) + break; + if (strcmp(modify->fix[i]->style,"npt/uef")==0) + break; + } + if (i==modify->nfix) + error->all(FLERR,"Can't use dump cfg/uef without defining a fix nvt/npt/uef"); + ifix_uef=i; +} + +/* ---------------------------------------------------------------------- + * this is really the only difference between the base class and this one. + * since the output is in scaled coordinates, changing the simulation box + * edges to the flow frame will put coordinates in the flow frame too. + * ----------------------------------------------------------------------*/ + +void DumpCFGUef::write_header(bigint n) +{ + // set scale factor used by AtomEye for CFG viz + // default = 1.0 + // for peridynamics, set to pre-computed PD scale factor + // so PD particles mimic C atoms + // for unwrapped coords, set to UNWRAPEXPAND (10.0) + // so molecules are not split across periodic box boundaries + + double box[3][3],rot[3][3]; + ((FixNHUef*) modify->fix[ifix_uef])->get_box(box); + ((FixNHUef*) modify->fix[ifix_uef])->get_rot(rot); + // rot goes from "lab frame" to "upper triangular frame" + // it's transpose takes the simulation box to the flow frame + for (int i=0;i<3;i++) + for(int j=i+1;j<3;j++) + { + double t=rot[i][j]; + rot[i][j]=rot[j][i]; + rot[j][i]=t; + } + mul_m2(rot,box); + + + double scale = 1.0; + if (atom->peri_flag) scale = atom->pdscale; + else if (unwrapflag == 1) scale = UNWRAPEXPAND; + + char str[64]; + sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT); + fprintf(fp,str,n); + fprintf(fp,"A = %g Angstrom (basic length-scale)\n",scale); + // in box[][] columns are cell edges + // in H0, rows are cell edges + fprintf(fp,"H0(1,1) = %g A\n",box[0][0]); + fprintf(fp,"H0(1,2) = %g A\n",box[1][0]); + fprintf(fp,"H0(1,3) = %g A\n",box[2][0]); + fprintf(fp,"H0(2,1) = %g A\n",box[0][1]); + fprintf(fp,"H0(2,2) = %g A\n",box[1][1]); + fprintf(fp,"H0(2,3) = %g A\n",box[2][1]); + fprintf(fp,"H0(3,1) = %g A\n",box[0][2]); + fprintf(fp,"H0(3,2) = %g A\n",box[1][2]); + fprintf(fp,"H0(3,3) = %g A\n",box[2][2]); + fprintf(fp,".NO_VELOCITY.\n"); + fprintf(fp,"entry_count = %d\n",nfield-2); + for (int i = 0; i < nfield-5; i++) + fprintf(fp,"auxiliary[%d] = %s\n",i,auxname[i]); +} diff --git a/src/USER-UEF/dump_cfg_uef.h b/src/USER-UEF/dump_cfg_uef.h new file mode 100644 index 0000000000..059fc63008 --- /dev/null +++ b/src/USER-UEF/dump_cfg_uef.h @@ -0,0 +1,51 @@ +/* -*- 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. + + Contributing Author: David Nicholson (MIT) +------------------------------------------------------------------------- */ + +#ifdef DUMP_CLASS + +DumpStyle(cfg/uef,DumpCFGUef) + +#else + +#ifndef LMP_DUMP_CFG_UEF_H +#define LMP_DUMP_CFG_UEF_H + +#include "dump_cfg.h" + +namespace LAMMPS_NS { + +class DumpCFGUef : public DumpCFG { + public: + DumpCFGUef(LAMMPS *lmp, int narg, char **arg) : + DumpCFG(lmp, narg, arg){} + void init_style(); + void write_header(bigint); + + protected: + int ifix_uef; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Can't use dump cfg/uef without defining a fix nvt/npt/uef + +Self-explanatory. + +*/ diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp new file mode 100644 index 0000000000..74d4e78746 --- /dev/null +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -0,0 +1,846 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + www.cs.sandia.gov/~sjplimp/lammps.html + Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + + 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. + + Contributing author: David Nicholson (MIT) +------------------------------------------------------------------------- */ + +#include "string.h" +#include "stdlib.h" +#include "math.h" +#include "fix_nh_uef.h" +#include "atom.h" +#include "force.h" +#include "group.h" +#include "comm.h" +#include "irregular.h" +#include "modify.h" +#include "compute.h" +#include "kspace.h" +#include "update.h" +#include "domain.h" +#include "error.h" +#include "output.h" +#include "timer.h" +#include "neighbor.h" +#include "compute_pressure_uef.h" +#include "compute_temp_uef.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +enum{ISO,ANISO,TRICLINIC}; +/* ---------------------------------------------------------------------- + Put all of the uef-only keywords at the back of arg and make narg smaller + so FixNH::FixNH() only sees the keywords it knows. Save the numer of + remaining keywords in rem. + ---------------------------------------------------------------------- */ +char ** FixNHUef::arg_kludge(int &narg, char **arg, int &rem) +{ + int iarg = 3; + bool flags[3]= {false,false,false}; + rem=0; + char *tmp[3]; + while (iarg < narg) + { + if (strcmp(arg[iarg],"erate" ) == 0 && !flags[0]) + { + tmp[0] = arg[iarg]; + tmp[1] = arg[iarg+1]; + tmp[2] = arg[iarg+2]; + for (int k=iarg+3; k narg) error->all(FLERR,"Illegal fix nvt/npt/uef command"); + erate[0] = force->numeric(FLERR,arg[iarg+1]); + erate[1] = force->numeric(FLERR,arg[iarg+2]); + erate_flag = true; + iarg += 3; + } + else if (strcmp(arg[iarg],"strain")==0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal fix nvt/npt/uef command"); + strain[0] = force->numeric(FLERR,arg[iarg+1]); + strain[1] = force->numeric(FLERR,arg[iarg+2]); + iarg += 3; + } + else if (strcmp(arg[iarg],"ext")==0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/uef command"); + if (strcmp(arg[iarg+1],"x")==0) + ext_flags[1] = ext_flags[2] = false; + else if (strcmp(arg[iarg+1],"y")==0) + ext_flags[0] = ext_flags[2] = false; + else if (strcmp(arg[iarg+1],"z")==0) + ext_flags[0] = ext_flags[1] = false; + else if (strcmp(arg[iarg+1],"xy")==0) + ext_flags[2] = false; + else if (strcmp(arg[iarg+1],"xz")==0) + ext_flags[1] = false; + else if (strcmp(arg[iarg+1],"yz")==0) + ext_flags[0] = false; + else if (strcmp(arg[iarg+1],"xyz")!=0) + error->all(FLERR,"Illegal fix nvt/npt/uef command"); + + iarg += 2; + } + else + error->all(FLERR,"Illegal fix nvt/npt/uef command"); + } + if (!erate_flag) + error->all(FLERR,"Keyword erate must be set for fix npt/npt/uef command"); + + if (mtchain_default_flag) mtchain=1; + + if (!domain->triclinic) + error->all(FLERR,"Simulation box must be triclinic for fix/nvt/npt/uef"); + + //check for conditions that impose a deviatoric stress + if (pstyle == TRICLINIC) + error->all(FLERR,"Only normal stresses can be controlled with fix/nvt/npt/uef"); + double erate_tmp[3]; + erate_tmp[0]=erate[0]; + erate_tmp[1]=erate[1]; + erate_tmp[2]=-erate[0]-erate[1]; + + if (pstyle == ANISO) + { + if (!(ext_flags[0] & ext_flags[1] & ext_flags[2])) + error->all(FLERR,"The ext keyword may only be used with iso pressure control"); + for (int k=0;k<3;k++) + for (int j=0;j<3;j++) + if (p_flag[k] && p_flag[j]) + { + double tol = 1e-6; + if ( !nearly_equal(p_start[k],p_start[j],tol) || !nearly_equal(p_stop[k],p_stop[j],tol)) + error->all(FLERR,"All controlled stresses must have the same value in fix/nvt/npt/uef"); + if ( !nearly_equal(erate_tmp[k],erate_tmp[j],tol) || !nearly_equal(erate_tmp[k],erate_tmp[j],tol)) + error->all(FLERR,"Dimensions with controlled stresses must have same strain rate in fix/nvt/npt/uef"); + } + } + // conditions that produce a deviatoric stress have already + // been eliminated. + deviatoric_flag=0; + + // need pre_exchange and irregular migration + pre_exchange_flag = 1; + irregular = new Irregular(lmp); + + // flag that I change the box here (in case of nvt) + box_change_shape = 1; + + // initialize the UEFBox class which computes the box at each step + uefbox = new UEF_utils::UEFBox(); + uefbox->set_strain(strain[0],strain[1]); + + // reset fixedpoint to the stagnation point. I don't allow fixedpoint + // to be set by the user. + fixedpoint[0] = domain->boxlo[0]; + fixedpoint[1] = domain->boxlo[1]; + fixedpoint[2] = domain->boxlo[2]; + + // Create temp and pressure computes for uef + int n = strlen(id) + 6; + id_temp = new char[n]; + strcpy(id_temp,id); + strcat(id_temp,"_temp"); + char **newarg = new char*[3]; + newarg[0] = id_temp; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "temp/uef"; + modify->add_compute(3,newarg); + delete [] newarg; + tcomputeflag = 1; + n = strlen(id) + 7; + id_press = new char[n]; + strcpy(id_press,id); + strcat(id_press,"_press"); + newarg = new char*[4]; + newarg[0] = id_press; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "pressure/uef"; + newarg[3] = id_temp; + modify->add_compute(4,newarg); + delete [] newarg; + pcomputeflag = 1; + + nevery = 1; + + +} + +/* ---------------------------------------------------------------------- + * Erase the UEFBox object and get rid of the pressure compute if the nvt + * version is being used. Everything else will be done in base destructor + * ---------------------------------------------------------------------- */ +FixNHUef::~FixNHUef() +{ + delete uefbox; + if (pcomputeflag && !pstat_flag) + { + modify->delete_compute(id_press); + delete [] id_press; + } +} + +/* ---------------------------------------------------------------------- + * Make the end_of_step() routine callable + * ---------------------------------------------------------------------- */ +int FixNHUef::setmask() +{ + int mask = FixNH::setmask(); + mask |= END_OF_STEP; + return mask; +} + +/* ---------------------------------------------------------------------- + * Run FixNH::init() and do more error checking. Set the pressure + * pointer in the case that the nvt version is used + * ---------------------------------------------------------------------- */ +void FixNHUef::init() +{ + FixNH::init(); + + + // find conflict with fix/deform or other box chaging fixes + for (int i=0; i < modify->nfix; i++) + { + if (strcmp(modify->fix[i]->id,id) != 0) + if (modify->fix[i]->box_change_shape != 0) + error->all(FLERR,"Can't use another fix which changes box shape with fix/nvt/npt/uef"); + } + + + // this will make the pressure compute for nvt + if (!pstat_flag) + if (pcomputeflag) + { + int icomp = modify->find_compute(id_press); + if (icomp<0) + error->all(FLERR,"Pressure ID for fix/nvt/uef doesn't exist"); + pressure = modify->compute[icomp]; + + } + if (strcmp(pressure->style,"pressure/uef") != 0) + error->all(FLERR,"Using fix nvt/npt/uef without a compute pressure/uef"); + if (strcmp(temperature->style,"temp/uef") != 0) + error->all(FLERR,"Using fix nvt/npt/uef without a compute temp/uef"); + +} + +/* ---------------------------------------------------------------------- + * Run FixNH::setup() make sure the box is OK and set the rotation matrix + * for the first step + * ---------------------------------------------------------------------- */ +void FixNHUef::setup(int j) +{ + double box[3][3]; + double vol = domain->xprd * domain->yprd * domain->zprd; + uefbox->get_box(box,vol); + double tol = 1e-4; + // ensure the box is ok for uef + bool isok = true; + isok &= nearly_equal(domain->h[0],box[0][0],tol); + isok &= nearly_equal(domain->h[1],box[1][1],tol); + isok &= nearly_equal(domain->h[2],box[2][2],tol); + isok &= nearly_equal(domain->xy,box[0][1],tol); + isok &= nearly_equal(domain->yz,box[1][2],tol); + isok &= nearly_equal(domain->xz,box[0][2],tol); + if (!isok) + error->all(FLERR,"Initial box is not close enough to the expected uef box"); + + uefbox->get_rot(rot); + ((ComputeTempUef*) temperature)->yes_rot(); + ((ComputePressureUef*) pressure)->in_fix = true; + ((ComputePressureUef*) pressure)->update_rot(); + FixNH::setup(j); +} + +/* ---------------------------------------------------------------------- + * rotate -> initial integration step -> rotate back + * ---------------------------------------------------------------------- */ +void FixNHUef::initial_integrate(int vflag) +{ + inv_rotate_x(rot); + inv_rotate_v(rot); + inv_rotate_f(rot); + ((ComputeTempUef*) temperature)->no_rot(); + FixNH::initial_integrate(vflag); + rotate_x(rot); + rotate_v(rot); + rotate_f(rot); + ((ComputeTempUef*) temperature)->yes_rot(); +} + +/* ---------------------------------------------------------------------- + * rotate -> initial integration step -> rotate back (RESPA) + * ---------------------------------------------------------------------- */ +void FixNHUef::initial_integrate_respa(int vflag, int ilevel, int iloop) +{ + inv_rotate_x(rot); + inv_rotate_v(rot); + inv_rotate_f(rot); + ((ComputeTempUef*) temperature)->no_rot(); + FixNH::initial_integrate_respa(vflag,ilevel,iloop); + rotate_x(rot); + rotate_v(rot); + rotate_f(rot); + ((ComputeTempUef*) temperature)->yes_rot(); +} + +/* ---------------------------------------------------------------------- + * rotate -> final integration step -> rotate back + * ---------------------------------------------------------------------- */ +void FixNHUef::final_integrate() +{ + // update rot here since it must directly follow the virial calculation + ((ComputePressureUef*) pressure)->update_rot(); + inv_rotate_v(rot); + inv_rotate_f(rot); + ((ComputeTempUef*) temperature)->no_rot(); + FixNH::final_integrate(); + rotate_v(rot); + rotate_f(rot); + ((ComputeTempUef*) temperature)->yes_rot(); +} + +/* ---------------------------------------------------------------------- + * at outer level: call this->final_integrate() + * at other levels: rotate -> 2nd verlet step -> rotate back + * ---------------------------------------------------------------------- */ +void FixNHUef::final_integrate_respa(int ilevel, int iloop) +{ + // set timesteps by level + dtf = 0.5 * step_respa[ilevel] * force->ftm2v; + dthalf = 0.5 * step_respa[ilevel]; + // outermost level - update eta_dot and omega_dot, apply via final_integrate + // all other levels - NVE update of v + if (ilevel == nlevels_respa-1) final_integrate(); + else + { + inv_rotate_v(rot); + inv_rotate_f(rot); + nve_v(); + rotate_v(rot); + rotate_f(rot); + } +} + +/* ---------------------------------------------------------------------- + SLLOD velocity update in time-reversible (i think) increments + v -> exp(-edot*dt/2)*v + v -> v +f/m*dt + v -> exp(-edot*dt/2)*v +-----------------------------------------------------------------------*/ +void FixNHUef::nve_v() +{ + double dtfm; + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double ex = erate[0]*dtf/2; + double ey = erate[1]*dtf/2; + double ez = -ex-ey; + double e0 = exp(-ex); + double e1 = exp(-ey); + double e2 = exp(-ez); + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + if (rmass) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + dtfm = dtf / rmass[i]; + v[i][0] *= e0; + v[i][1] *= e1; + v[i][2] *= e2; + v[i][0] += dtfm*f[i][0]; + v[i][1] += dtfm*f[i][1]; + v[i][2] += dtfm*f[i][2]; + v[i][0] *= e0; + v[i][1] *= e1; + v[i][2] *= e2; + } + } + } else { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + dtfm = dtf / mass[type[i]]; + v[i][0] *= e0; + v[i][1] *= e1; + v[i][2] *= e2; + v[i][0] += dtfm*f[i][0]; + v[i][1] += dtfm*f[i][1]; + v[i][2] += dtfm*f[i][2]; + v[i][0] *= e0; + v[i][1] *= e1; + v[i][2] *= e2; + } + } + } +} + +/* ---------------------------------------------------------------------- + Don't actually move atoms in remap(), just change the box +-----------------------------------------------------------------------*/ +void FixNHUef::remap() +{ + double vol = domain->xprd * domain->yprd * domain->zprd; + double domega = dto*(omega_dot[0]+omega_dot[1]+omega_dot[2])/3.; + + // constant volume strain associated with barostat + // box scaling + double ex = dto*omega_dot[0]-domega; + double ey = dto*omega_dot[1]-domega; + uefbox->step_deform(ex,ey); + strain[0] += ex; + strain[1] += ey; + + // volume change + vol = vol*exp(3*domega); + double box[3][3]; + uefbox->get_box(box,vol); + domain->boxhi[0] = domain->boxlo[0]+box[0][0]; + domain->boxhi[1] = domain->boxlo[1]+box[1][1]; + domain->boxhi[2] = domain->boxlo[2]+box[2][2]; + domain->xy = box[0][1]; + domain->xz = box[0][2]; + domain->yz = box[1][2]; + domain->set_global_box(); + domain->set_local_box(); + uefbox->get_rot(rot); +} + +/* ---------------------------------------------------------------------- + SLLOD position update in time-reversible (i think) increments + x -> exp(edot*dt/2)*x + x -> x + v*dt + x -> exp(edot*dt/2)*x +-----------------------------------------------------------------------*/ +void FixNHUef::nve_x() +{ + double **x = atom->x; + double **v = atom->v; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double ex = erate[0]*dtv; + strain[0] += ex; + double e0 = exp((ex+omega_dot[0]*dtv)/2); + double ey = erate[1]*dtv; + strain[1] += ey; + double e1 = exp((ey+omega_dot[1]*dtv)/2.); + double ez = -ex -ey; + double e2 = exp((ez+omega_dot[2]*dtv)/2.); + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + // x update by full step only for atoms in group + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + x[i][0] *= e0; + x[i][1] *= e1; + x[i][2] *= e2; + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + x[i][0] *= e0; + x[i][1] *= e1; + x[i][2] *= e2; + } + } + uefbox->step_deform(ex,ey); + double box[3][3]; + double vol = domain->xprd * domain->yprd * domain->zprd; + uefbox->get_box(box,vol); + domain->boxhi[0] = domain->boxlo[0]+box[0][0]; + domain->boxhi[1] = domain->boxlo[1]+box[1][1]; + domain->boxhi[2] = domain->boxlo[2]+box[2][2]; + domain->xy = box[0][1]; + domain->xz = box[0][2]; + domain->yz = box[1][2]; + domain->set_global_box(); + domain->set_local_box(); + uefbox->get_rot(rot); +} + +/* ---------------------------------------------------------------------- + * Do the lattice reduction if necessary. +-----------------------------------------------------------------------*/ +void FixNHUef::pre_exchange() +{ + // only need to reset things if the lattice needs to be reduced + if (uefbox->reduce()) + { + // go to lab frame + inv_rotate_x(rot); + inv_rotate_v(rot); + inv_rotate_f(rot); + // get & set the new box and rotation matrix + double vol = domain->xprd * domain->yprd * domain->zprd; + double box[3][3]; + uefbox->get_box(box,vol); + domain->boxhi[0] = domain->boxlo[0]+box[0][0]; + domain->boxhi[1] = domain->boxlo[1]+box[1][1]; + domain->boxhi[2] = domain->boxlo[2]+box[2][2]; + domain->xy = box[0][1]; + domain->xz = box[0][2]; + domain->yz = box[1][2]; + domain->set_global_box(); + domain->set_local_box(); + uefbox->get_rot(rot); + + // rotate to the new upper triangular frame + rotate_v(rot); + rotate_x(rot); + rotate_f(rot); + + // put all atoms in the new box + double **x = atom->x; + imageint *image = atom->image; + int nlocal = atom->nlocal; + for (int i=0; iremap(x[i],image[i]); + + // move atoms to the right processors + domain->x2lamda(atom->nlocal); + irregular->migrate_atoms(); + domain->lamda2x(atom->nlocal); + } +} + +/* ---------------------------------------------------------------------- + * The following are routines to rotate between the lab and upper triangular + * (UT) frames. For most of the time the simulation is in the UT frame. + * To get to the lab frame, apply the inv_rotate_[..](rot) and to + * get back to the UT frame apply rotate_[..](rot). + * + * Note: the rotate_x() functions also apply a shift to/from the fixedpoint + * to make the integration a little simpler. + * ---------------------------------------------------------------------- */ +void FixNHUef::rotate_x(double r[3][3]) +{ + double **x = atom->x; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + double xn[3]; + for (int i=0;iboxlo[0]; + x[i][1]=xn[1]+domain->boxlo[1]; + x[i][2]=xn[2]+domain->boxlo[2]; + } + } +} + +void FixNHUef::inv_rotate_x(double r[3][3]) +{ + double **x = atom->x; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + double xn[3]; + for (int i=0;iboxlo[0]; + x[i][1] -= domain->boxlo[1]; + x[i][2] -= domain->boxlo[2]; + xn[0]=r[0][0]*x[i][0]+r[1][0]*x[i][1]+r[2][0]*x[i][2]; + xn[1]=r[0][1]*x[i][0]+r[1][1]*x[i][1]+r[2][1]*x[i][2]; + xn[2]=r[0][2]*x[i][0]+r[1][2]*x[i][1]+r[2][2]*x[i][2]; + x[i][0]=xn[0]; + x[i][1]=xn[1]; + x[i][2]=xn[2]; + } + } +} + +void FixNHUef::rotate_v(double r[3][3]) +{ + double **v = atom->v; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + double vn[3]; + for (int i=0;iv; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + double vn[3]; + for (int i=0;if; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + double fn[3]; + for (int i=0;if; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + double fn[3]; + for (int i=0;iset_strain(strain[0],strain[1]); +} + +/* ---------------------------------------------------------------------- + * If the step writes a restart, reduce the box beforehand. This makes sure + * the unique box shape can be found once the restart is read and that + * all of the atoms lie within the box. + * This may only be necessary for RESPA runs, but I'm leaving it in anyway. + * ---------------------------------------------------------------------- */ +void FixNHUef::end_of_step() +{ + if (update->ntimestep==output->next_restart) + { + pre_exchange(); + domain->x2lamda(atom->nlocal); + domain->pbc(); + timer->stamp(); + comm->exchange(); + comm->borders(); + domain->lamda2x(atom->nlocal+atom->nghost); + timer->stamp(Timer::COMM); + neighbor->build(); + timer->stamp(Timer::NEIGH); + } +} + +/* ---------------------------------------------------------------------- + * reduce the simulation box after a run is complete. otherwise it won't + * be possible to resume from a write_restart since the initialization of + * the simulation box requires reduced simulation box + * ---------------------------------------------------------------------- */ +void FixNHUef::post_run() +{ + pre_exchange(); + domain->x2lamda(atom->nlocal); + domain->pbc(); + timer->stamp(); + comm->exchange(); + comm->borders(); + domain->lamda2x(atom->nlocal+atom->nghost); + timer->stamp(Timer::COMM); + neighbor->build(); + timer->stamp(Timer::NEIGH); +} + +/* ---------------------------------------------------------------------- + * public read for rotation matrix + * ---------------------------------------------------------------------- */ +void FixNHUef::get_rot(double r[3][3]) +{ + r[0][0] = rot[0][0]; + r[0][1] = rot[0][1]; + r[0][2] = rot[0][2]; + r[1][0] = rot[1][0]; + r[1][1] = rot[1][1]; + r[1][2] = rot[1][2]; + r[2][0] = rot[2][0]; + r[2][1] = rot[2][1]; + r[2][2] = rot[2][2]; +} + +/* ---------------------------------------------------------------------- + * public read for ext flags + * ---------------------------------------------------------------------- */ +void FixNHUef::get_ext_flags(bool* e) +{ + e[0] = ext_flags[0]; + e[1] = ext_flags[1]; + e[2] = ext_flags[2]; +} + +/* ---------------------------------------------------------------------- + * public read for simulation box + * ---------------------------------------------------------------------- */ +void FixNHUef::get_box(double b[3][3]) +{ + double box[3][3]; + double vol = domain->xprd * domain->yprd * domain->zprd; + uefbox->get_box(box,vol); + b[0][0] = box[0][0]; + b[0][1] = box[0][1]; + b[0][2] = box[0][2]; + b[1][0] = box[1][0]; + b[1][1] = box[1][1]; + b[1][2] = box[1][2]; + b[2][0] = box[2][0]; + b[2][1] = box[2][1]; + b[2][2] = box[2][2]; +} + +/* ---------------------------------------------------------------------- + * comparing floats + * it's imperfect, but should work provided no infinities + * ---------------------------------------------------------------------- */ +bool FixNHUef::nearly_equal(double a, double b, double epsilon) +{ + double absa = fabs(a); + double absb = fabs(b); + double diff = fabs(a-b); + if (a == b) return true; + else if ( (absa+absb) < epsilon) + return diff < epsilon*epsilon; + else + return diff/(absa+absb) < epsilon; +} diff --git a/src/USER-UEF/fix_nh_uef.h b/src/USER-UEF/fix_nh_uef.h new file mode 100644 index 0000000000..46916005a3 --- /dev/null +++ b/src/USER-UEF/fix_nh_uef.h @@ -0,0 +1,125 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + www.cs.sandia.gov/~sjplimp/lammps.html + Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + + 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. + + Contributing Author: David Nicholson (MIT) +------------------------------------------------------------------------- */ + + +#ifndef LMP_FIX_NH_UEF_H +#define LMP_FIX_NH_UEF_H + +#include "uef_utils.h" +#include "fix_nh.h" + +namespace LAMMPS_NS { +class FixNHUef : public FixNH { + public: + FixNHUef(class LAMMPS *, int, char **); + virtual ~FixNHUef(); + virtual int setmask(); + virtual void init(); + virtual void setup(int); + virtual void pre_exchange(); + virtual int pack_restart_data(double*); + virtual void restart(char *); + virtual void end_of_step(); + virtual void initial_integrate(int); + virtual void final_integrate(); + virtual void initial_integrate_respa(int, int, int); + virtual void final_integrate_respa(int, int); + virtual void post_run(); + void get_rot(double[3][3]); + void get_ext_flags(bool*); + void get_box(double[3][3]); + + protected: + virtual void remap(); + virtual int size_restart_global(); + virtual void nve_x(); + virtual void nve_v(); + char **arg_kludge(int&, char**, int&); + void rotate_x(double [3][3]); + void inv_rotate_x(double[3][3]); + void rotate_v(double[3][3]); + void inv_rotate_v(double[3][3]); + void rotate_f(double[3][3]); + void inv_rotate_f(double[3][3]); + double strain[2],erate[2]; // strain/strain rate : [e_x, e_y] + // always assume traceless e_z = -e_x-e_y + + int rem; //this is for the narg kluge + + UEF_utils::UEFBox *uefbox; // interface for the special simulation box + + double rot[3][3]; // rotation matrix + bool ext_flags[3]; // flags for external "free surfaces" + bool nearly_equal(double,double,double); + //bool rotate_output; // experimental feature. Too many issues for now +}; + +} + +#endif + +/* ERROR/WARNING messages: + +This is a base class for FixNH so it will inherit most of its error/warning messages along with the following: + +E: Illegal fix nvt/npt/uef command + +Self-explanatory + +E: Keyword erate must be set for fix nvt/npt/uef command + +Self-explanatory. + +E: Simulation box must be triclinic for fix/nvt/npt/uef + +Self-explanatory. + +E: Only normal stresses can be controlled with fix/nvt/npt/uef + +The keywords xy xz and yz cannot be used for pressure control + +E: The ext keyword may only be used with iso pressure control + +Self-explanatory + +E: All controlled stresses must have the same value in fix/nvt/npt/uef + +Stress control is only possible when the stress specified for each dimension is the same + +E: Dimensions with controlled stresses must have same strain rate in fix/nvt/npt/uef + +Stress-controlled dimensions with the same strain rate must have the same target stress. + +E: Can't use another fix which changes box shape with fix/nvt/npt/uef + +The fix npt/nvt/uef command must have full control over the box shape. You cannot use a simultaneous fix deform command, for example. + +E: Pressure ID for fix/nvt/uef doesn't exist + +The compute pressure introduced via fix_modify does not exist + +E: Using fix nvt/npt/uef without a compute pressure/uef + +Self-explanatory. + +E: Using fix nvt/npt/uef without a compute temp/uef + +Self-explanatory. + +E: Initial box is not close enough to the expected uef box + +The initial box does not correspond to the shape required by the value of the strain keyword. If the default strain value of zero was used, the initial box is not cubic. + +*/ diff --git a/src/USER-UEF/fix_npt_uef.cpp b/src/USER-UEF/fix_npt_uef.cpp new file mode 100644 index 0000000000..1bf027bf85 --- /dev/null +++ b/src/USER-UEF/fix_npt_uef.cpp @@ -0,0 +1,33 @@ +/* ---------------------------------------------------------------------- + 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. + + Contributing author: David Nicholson (MIT) +------------------------------------------------------------------------- */ + +#include "string.h" +#include "fix_npt_uef.h" +#include "modify.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + + +FixNPTUef::FixNPTUef(LAMMPS *lmp, int narg, char **arg) : + FixNHUef(lmp, narg, arg) +{ + if (!tstat_flag) + error->all(FLERR,"Temperature control must be used with fix npt/uef"); + if (!pstat_flag) + error->all(FLERR,"Pressure control must be used with fix npt/uef"); + +} diff --git a/src/USER-UEF/fix_npt_uef.h b/src/USER-UEF/fix_npt_uef.h new file mode 100644 index 0000000000..a77060a937 --- /dev/null +++ b/src/USER-UEF/fix_npt_uef.h @@ -0,0 +1,50 @@ +/* ---------------------------------------------------------------------- + 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. + + Contributing author: David Nicholson (MIT) +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(npt/uef,FixNPTUef) + +#else + +#ifndef LMP_FIX_NPT_UEF_H +#define LMP_FIX_NPT_UEF_H + +#include "fix_nh_uef.h" + +namespace LAMMPS_NS { + +class FixNPTUef : public FixNHUef { + public: + FixNPTUef(class LAMMPS *, int, char **); + ~FixNPTUef() {} +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Temperature control must be used with fix npt uef + +Self-explanatory. + +E: Pressure control must be used with fix npt uef + +Self-explanatory. + +*/ diff --git a/src/USER-UEF/fix_nvt_uef.cpp b/src/USER-UEF/fix_nvt_uef.cpp new file mode 100644 index 0000000000..589a4b5b56 --- /dev/null +++ b/src/USER-UEF/fix_nvt_uef.cpp @@ -0,0 +1,35 @@ +/* ---------------------------------------------------------------------- + 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. + + Contributing author: David Nicholson (MIT) +------------------------------------------------------------------------- */ + +#include "string.h" +#include "fix_nvt_uef.h" +#include "modify.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + + +FixNVTUef::FixNVTUef(LAMMPS *lmp, int narg, char **arg) : + FixNHUef(lmp, narg, arg) +{ + if (!tstat_flag) + error->all(FLERR,"Temperature control must be used with fix nvt/uef"); + if (pstat_flag) + error->all(FLERR,"Pressure control can't be used with fix nvt/uef"); + +} + + diff --git a/src/USER-UEF/fix_nvt_uef.h b/src/USER-UEF/fix_nvt_uef.h new file mode 100644 index 0000000000..a6eba7a284 --- /dev/null +++ b/src/USER-UEF/fix_nvt_uef.h @@ -0,0 +1,50 @@ +/* ---------------------------------------------------------------------- + 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. + + Contributing author: David Nicholson (MIT) +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(nvt/uef,FixNVTUef) + +#else + +#ifndef LMP_FIX_NVT_UEF_H +#define LMP_FIX_NVT_UEF_H + +#include "fix_nh_uef.h" + +namespace LAMMPS_NS { + +class FixNVTUef : public FixNHUef { + public: + FixNVTUef(class LAMMPS *, int, char **); + ~FixNVTUef(){} +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Temperature control must be used with fix npt uef + +Self-explanatory. + +E: Pressure control must be used with fix npt uef + +Self-explanatory. + +*/ diff --git a/src/USER-UEF/uef_utils.cpp b/src/USER-UEF/uef_utils.cpp new file mode 100644 index 0000000000..93bbd2b77d --- /dev/null +++ b/src/USER-UEF/uef_utils.cpp @@ -0,0 +1,365 @@ +/* ---------------------------------------------------------------------- + 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. + + Contributing author: David Nicholson (MIT) +------------------------------------------------------------------------- + + This class contains functions to calculate the evolution of the periodic + simulation box under elongational flow as described by Matthew Dobson + in the arXiv preprint at http://arxiv.org/abs/1408.7078 + + Additionally, there are methods to do a lattice reduction to further + reduce the simulation box using the method of Igor Semaev at + http://link.springer.com/chapter/10.1007%2F3-540-44670-2_13 +*/ +#include +#include "uef_utils.h" + +using namespace LAMMPS_NS; +using namespace UEF_utils; + +UEFBox::UEFBox() +{ + // initial box (also an inverse eigenvector matrix of automorphisms) + double x = 0.327985277605681; + double y = 0.591009048506103; + double z = 0.736976229099578; + l0[0][0]= z; l0[0][1]= y; l0[0][2]= x; + l0[1][0]=-x; l0[1][1]= z; l0[1][2]=-y; + l0[2][0]=-y; l0[2][1]= x; l0[2][2]= z; + // spectra of the two automorpisms (log of eigenvalues) + w1[0]=-1.177725211523360; + w1[1]=-0.441448620566067; + w1[2]= 1.619173832089425; + w2[0]= w1[1]; + w2[1]= w1[2]; + w2[2]= w1[0]; + // initialize theta + // strain = w1 * theta1 + w2 * theta2 + theta[0]=theta[1]=0; + + + //set up the initial box l and change of basis matrix r + for (int k=0;k<3;k++) + for (int j=0;j<3;j++) + { + l[k][j] = l0[k][j]; + r[j][k]=(j==k); + } + + // get the initial rotation and upper triangular matrix + rotation_matrix(rot, lrot ,l); + + // this is just a way to calculate the automorphisms + // themselves, which play a minor role in the calculations + // it's overkill, but only called once + double t1[3][3]; + double t1i[3][3]; + double t2[3][3]; + double t2i[3][3]; + double l0t[3][3]; + for (int k=0; k<3; ++k) + for (int j=0; j<3; ++j) + { + t1[k][j] = exp(w1[k])*l0[k][j]; + t1i[k][j] = exp(-w1[k])*l0[k][j]; + t2[k][j] = exp(w2[k])*l0[k][j]; + t2i[k][j] = exp(-w2[k])*l0[k][j]; + l0t[k][j] = l0[j][k]; + } + mul_m2(l0t,t1); + mul_m2(l0t,t1i); + mul_m2(l0t,t2); + mul_m2(l0t,t2i); + for (int k=0; k<3; ++k) + for (int j=0; j<3; ++j) + { + a1[k][j] = round(t1[k][j]); + a1i[k][j] = round(t1i[k][j]); + a2[k][j] = round(t2[k][j]); + a2i[k][j] = round(t2i[k][j]); + } + + // winv used to transform between + // strain increments and theta increments + winv[0][0] = w2[1]; + winv[0][1] = -w2[0]; + winv[1][0] = -w1[1]; + winv[1][1] = w1[0]; + double d = w1[0]*w2[1] - w2[0]*w1[1]; + for (int k=0;k<2;k++) + for (int j=0;j<2;j++) + winv[k][j] /= d; +} + +// get volume-correct r basis in: basis*cbrt(vol) = q*r +void UEFBox::get_box(double x[3][3], double v) +{ + v = cbrtf(v); + for (int k=0;k<3;k++) + for (int j=0;j<3;j++) + x[k][j] = lrot[k][j]*v; +} + +// get rotation matrix q in: basis = q*r +void UEFBox::get_rot(double x[3][3]) +{ + for (int k=0;k<3;k++) + for (int j=0;j<3;j++) + x[k][j]=rot[k][j]; +} + +// diagonal, incompressible deformation +void UEFBox::step_deform(const double ex, const double ey) +{ + // increment theta values used in the reduction + theta[0] +=winv[0][0]*ex + winv[0][1]*ey; + theta[1] +=winv[1][0]*ex + winv[1][1]*ey; + + // deformation of the box. reduce() needs to + // be called regularly or calculation will become + // unstable + double eps[3]; + eps[0]=ex; eps[1] = ey; eps[2] = -ex-ey; + for (int k=0;k<3;k++) + { + eps[k] = exp(eps[k]); + l[k][0] = eps[k]*l[k][0]; + l[k][1] = eps[k]*l[k][1]; + l[k][2] = eps[k]*l[k][2]; + } + rotation_matrix(rot,lrot, l); +} +// reuduce the current basis +bool UEFBox::reduce() +{ + // determine how many times to apply the automorphisms + // and find new theta values + int f1 = round(theta[0]); + int f2 = round(theta[1]); + theta[0] -= f1; + theta[1] -= f2; + + // store old change or basis matrix to determine if it + // changes + int r0[3][3]; + for (int k=0;k<3;k++) + for (int j=0;j<3;j++) + r0[k][j]=r[k][j]; + + // this modifies the old change basis matrix to + // handle the case where the automorphism transforms + // the box but the reduced basis doesn't change + // (r0 should still equal r at the end) + if (f1 > 0) for (int k=0;k 0) for (int k=0;k (-q)*m = (-r) will hold row-wise + if (r[0][0] < 0){ neg_row(q,0); neg_row(r,0); } + if (r[1][1] < 0){ neg_row(q,1); neg_row(r,1); } + if (r[2][2] < 0){ neg_row(q,2); neg_row(r,2); } +} + + + +//sort columns in order of increasing length +void col_sort(double b[3][3],int r[3][3]) +{ + if (col_prod(b,0,0)>col_prod(b,1,1)) + { + col_swap(b,0,1); + col_swap(r,0,1); + } + if (col_prod(b,0,0)>col_prod(b,2,2)) + { + col_swap(b,0,2); + col_swap(r,0,2); + } + if (col_prod(b,1,1)>col_prod(b,2,2)) + { + col_swap(b,1,2); + col_swap(r,1,2); + } +} + + +// 1-2 reduction (Graham-Schmidt) +void red12(double b[3][3],int r[3][3]) +{ + int y = round(col_prod(b,0,1)/col_prod(b,0,0)); + b[0][1] -= y*b[0][0]; + b[1][1] -= y*b[1][0]; + b[2][1] -= y*b[2][0]; + + r[0][1] -= y*r[0][0]; + r[1][1] -= y*r[1][0]; + r[2][1] -= y*r[2][0]; + if (col_prod(b,1,1) < col_prod(b,0,0)) + { + col_swap(b,0,1); + col_swap(r,0,1); + red12(b,r); + } +} + +// The Semaev condition for a 3-reduced basis +void red3(double b[3][3], int r[3][3]) +{ + double b11 = col_prod(b,0,0); + double b22 = col_prod(b,1,1); + double b12 = col_prod(b,0,1); + double b13 = col_prod(b,0,2); + double b23 = col_prod(b,1,2); + + double y2 =-(b23/b22-b12/b22*b13/b11)/(1-b12/b11*b12/b22); + double y1 =-(b13/b11-b12/b11*b23/b22)/(1-b12/b11*b12/b22); + + int x1=0; + int x2=0; + double min = col_prod(b,2,2); + int x1v[2]; + int x2v[2]; + x1v[0] = floor(y1); x1v[1] = x1v[0]+1; + x2v[0] = floor(y2); x2v[1] = x2v[0]+1; + for (int k=0;k<2;k++) + for (int j=0;j<2;j++) + { + double a[3]; + a[0] = b[0][2] + x1v[k]*b[0][0] + x2v[j]*b[0][1]; + a[1] = b[1][2] + x1v[k]*b[1][0] + x2v[j]*b[1][1]; + a[2] = b[2][2] + x1v[k]*b[2][0] + x2v[j]*b[2][1]; + double val=a[0]*a[0]+a[1]*a[1]+a[2]*a[2]; + if (val +T col_prod(T x[3][3], int c1, int c2) +{ + return x[0][c1]*x[0][c2]+x[1][c1]*x[1][c2]+x[2][c1]*x[2][c2]; +} + +template +void col_swap(T x[3][3], int c1, int c2) +{ + for (int k=0;k<3;k++) + { + T t = x[k][c2]; + x[k][c2]=x[k][c1]; + x[k][c1]=t; + } +} + +template +void neg_col(T x[3][3], int c1) +{ + x[0][c1] = -x[0][c1]; + x[1][c1] = -x[1][c1]; + x[2][c1] = -x[2][c1]; +} + +template +void neg_row(T x[3][3], int c1) +{ + x[c1][0] = -x[c1][0]; + x[c1][1] = -x[c1][1]; + x[c1][2] = -x[c1][2]; +} + +template +T det(T x[3][3]) +{ + double val; + val = x[0][0]*(x[1][1]*x[2][2] - x[1][2]*x[2][1]); + val -= x[0][1]*(x[1][0]*x[2][2] - x[1][2]*x[2][0]); + val += x[0][2]*(x[1][0]*x[2][1] - x[1][1]*x[2][0]); + return val; +} + +template +bool mat_same(T x1[3][3], T x2[3][3]) +{ + bool v = true; + for (int k=0;k<3;k++) + for (int j=0;j<3;j++) + v &= (x1[k][j]==x2[k][j]); + return v; +} + +template +void mul_m1(T m1[3][3], const T m2[3][3]) +{ + T t[3][3]; + for (int k=0;k<3;k++) + for (int j=0;j<3;j++) + t[k][j]=m1[k][j]; + + for (int k=0;k<3;k++) + for (int j=0;j<3;j++) + m1[k][j] = t[k][0]*m2[0][j] + t[k][1]*m2[1][j] + t[k][2]*m2[2][j]; +} + +template +void mul_m2(const T m1[3][3], T m2[3][3]) +{ + T t[3][3]; + for (int k=0;k<3;k++) + for (int j=0;j<3;j++) + t[k][j]=m2[k][j]; + + for (int k=0;k<3;k++) + for (int j=0;j<3;j++) + m2[k][j] = m1[k][0]*t[0][j] + m1[k][1]*t[1][j] + m1[k][2]*t[2][j]; +} + +} +} From 80898b86959ccac5d98298dd98fd4ddb331d95bc Mon Sep 17 00:00:00 2001 From: David Nicholson Date: Thu, 28 Sep 2017 17:42:02 -0400 Subject: [PATCH 02/21] first draft of doc done --- doc/src/dump_cfg_uef.txt | 53 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 doc/src/dump_cfg_uef.txt diff --git a/doc/src/dump_cfg_uef.txt b/doc/src/dump_cfg_uef.txt new file mode 100644 index 0000000000..a857ea4820 --- /dev/null +++ b/doc/src/dump_cfg_uef.txt @@ -0,0 +1,53 @@ + "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +dump cfg/uef command :h3 + +[Syntax:] + +dump ID group-ID cfg/uef N file mass type xs ys zs args :pre + +ID = user-assigned name for the dump :ulb,l +group-ID = ID of the group of atoms to be dumped :l +N = dump every this many timesteps :l +file = name of file to write dump info to :l +args = same as args for "dump custom"_dump.html :pre + +:ule + +[Examples:] + +dump 1 all cfg/uef 10 dump.*.cfg mass type xs ys zs +dump 2 all cfg/uef 100 dump.*.cfg mass type xs ys zs id c_stress + +[Description:] + +This command is used to dump atomic coordinates in the +reference frame of the applied flow field when +"fix nvt/uef"_fix_nh_uef.html or +"fix npt/uef"_fix_nh_uef.html or is used. Only the atomic +coordinates and frame-invariant scalar quantities +will be in the flow frame. If velocities are selected +as output, for example, they will not be in the same +reference frame as the atomic positions. + +[Restrictions:] + +This fix is part of the USER-UEF package. It is only enabled if +LAMMPS was built with that package. See the +"Making LAMMPS"_Section_start.html#start_3 section for more info. + +This command can only be used when "fix nvt/uef"_fix_nh_uef.html +or "fix npt/uef"_fix_nh_uef.html is active. + +[Related commands:] + +"dump"_dump.html, +"fix nvt/uef"_fix_nh_uef.html + +[Default:] none From c0f1a326616a3338521491de9307db4dcc694f7d Mon Sep 17 00:00:00 2001 From: David Nicholson Date: Thu, 28 Sep 2017 17:43:59 -0400 Subject: [PATCH 03/21] fixed namespace issue --- src/USER-UEF/dump_cfg_uef.cpp | 3 ++- src/USER-UEF/uef_utils.cpp | 5 ++--- src/USER-UEF/uef_utils.h | 6 ++++-- 3 files changed, 8 insertions(+), 6 deletions(-) diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/USER-UEF/dump_cfg_uef.cpp index 2ee216934c..44e1f8c5ae 100644 --- a/src/USER-UEF/dump_cfg_uef.cpp +++ b/src/USER-UEF/dump_cfg_uef.cpp @@ -24,6 +24,7 @@ #include "compute.h" #include "fix.h" #include "error.h" +#include "uef_utils.h" #include "dump_cfg_uef.h" #include "fix_nh_uef.h" @@ -84,7 +85,7 @@ void DumpCFGUef::write_header(bigint n) rot[i][j]=rot[j][i]; rot[j][i]=t; } - mul_m2(rot,box); + UEF_utils::mul_m2(rot,box); double scale = 1.0; diff --git a/src/USER-UEF/uef_utils.cpp b/src/USER-UEF/uef_utils.cpp index 93bbd2b77d..37ee896c7e 100644 --- a/src/USER-UEF/uef_utils.cpp +++ b/src/USER-UEF/uef_utils.cpp @@ -24,8 +24,7 @@ #include #include "uef_utils.h" -using namespace LAMMPS_NS; -using namespace UEF_utils; +namespace LAMMPS_NS{ namespace UEF_utils{ UEFBox::UEFBox() { @@ -362,4 +361,4 @@ void make_unique(double b[3][3], int r[3][3]) if (b[1][1] < 0){ neg_col(b,1); neg_col(r,1); } if (det(b) < 0){ neg_col(b,2); neg_col(r,2); } } - +}} diff --git a/src/USER-UEF/uef_utils.h b/src/USER-UEF/uef_utils.h index 94527a49b3..e3aefec2ef 100644 --- a/src/USER-UEF/uef_utils.h +++ b/src/USER-UEF/uef_utils.h @@ -23,9 +23,10 @@ http://link.springer.com/chapter/10.1007%2F3-540-44670-2_13 */ +#ifndef UEF_UTILS_H +#define UEF_UTILS_H -namespace LAMMPS_NS { -namespace UEF_utils { +namespace LAMMPS_NS{ namespace UEF_utils{ class UEFBox { @@ -137,3 +138,4 @@ void mul_m2(const T m1[3][3], T m2[3][3]) } } +#endif From 0029583463c1da81908bd324f55208d5972a0d22 Mon Sep 17 00:00:00 2001 From: David Nicholson Date: Thu, 28 Sep 2017 17:46:39 -0400 Subject: [PATCH 04/21] doc edits i missed in earlier commit --- doc/src/JPG/uef_frames.jpg | Bin 0 -> 12271 bytes doc/src/Section_commands.txt | 4 +- doc/src/Section_packages.txt | 7 +- doc/src/compute_pressure_uef.txt | 61 +++ doc/src/compute_temp_uef.txt | 18 +- doc/src/computes.txt | 2 + doc/src/dump_cfg_uef.txt | 2 +- doc/src/fix_nh_uef.txt | 683 ++++--------------------------- doc/src/fixes.txt | 1 + 9 files changed, 168 insertions(+), 610 deletions(-) create mode 100644 doc/src/JPG/uef_frames.jpg create mode 100644 doc/src/compute_pressure_uef.txt diff --git a/doc/src/JPG/uef_frames.jpg b/doc/src/JPG/uef_frames.jpg new file mode 100644 index 0000000000000000000000000000000000000000..3b3bfc3a245de1b00d594f865b9c93f1149deffd GIT 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zmjcxEvvl6Ik&l-%t_)&d;(lBbV)M1g_U!ie;m9~G1(0_v_`UJ)zTl~D3nDlPN)=aW zL1=>Yfj427Af5!G)mQgT3-*&OgScvZ?3H5Mb~7Tv^)_O3^K^@DqKeZRUvn}~I7;#9 z1L%vcYw0K1C?0G}U@cb*7o-8~bvcpumcJf+B?Jcz+38Mx`u<6>2)IMyb8d9AuWFbW_^oRYG>}+Ue~8_KTy5i ztR)Xkd*L z5~GC)840aweVsF1Fwe7kX6nIUu;;BE2X@{m6a;4o(Dx~-YU^if^eZ-Z*eHniKQhmL z0lOv)R2mXJ)S9Z-s75fc1u6C*toX4+oM%tI5r;)6h5&6!*h(VUjuk?kz=Edcx z{c5=Ddlw$a(G*x!*2aeLgT~B@;%K;b_5ZMn-H?|vUmB{B4p`wQw#G%Ip)OM#+9uDv z(6qauAKQ1`Qf$8Y=feYX-p=)|L#!Qbqhj!kf0!C8QSV+Cx+VRw-1>|-j$-noT+OU2 z1M|}9s~%qt8COT50m3w*h1lnE>Jo(a;x+sF*J(JF#RuBiaj9EeYX*vq^tfhh(%WKb z+vHC`|EjNwhU0TTVGw6GMXjReIOqk1LCF)Ka-1;w1gMAKRHgS3`bqyz-oKEHBzZ`hpUprum4=^{%^;L=4tu=02NVdW&i*H literal 0 HcmV?d00001 diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 3ac9c05e5c..fd7d6b4399 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -715,13 +715,13 @@ package"_Section_start.html#start_3. "nve/manifold/rattle"_fix_nve_manifold_rattle.html, "nvk"_fix_nvk.html, "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, -"nvt/uef"_fix_nh_uef.html, "nph/eff"_fix_nh_eff.html, "npt/eff"_fix_nh_eff.html, -"npt/uef"_fix_nh_uef.html, "nve/eff"_fix_nve_eff.html, "nvt/eff"_fix_nh_eff.html, "nvt/sllod/eff"_fix_nvt_sllod_eff.html, +"npt/uef"_fix_nh_uef.html, +"nvt/uef"_fix_nh_uef.html, "phonon"_fix_phonon.html, "pimd"_fix_pimd.html, "qbmsst"_fix_qbmsst.html, diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index 45cdd8ff48..58e41fc4ed 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -150,7 +150,7 @@ Package, Description, Doc page, Example, Library "USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, - "USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, - "USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, - -"USER-UEF"_#USER-UEF, NEMD under extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, - +"USER-UEF"_#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, - "USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l) :line @@ -2771,7 +2771,7 @@ examples/USER/tally :ul :line -UEF package :link(UEF),h4 +USER-UEF package :link(USER-UEF),h4 [Contents:] @@ -2779,6 +2779,8 @@ A fix style for the integration of the equations of motion under extensional flow with proper boundary conditions, as well as several supporting compute styles and an output option. +[Author:] David Nicholson (MIT). + [Install or un-install:] make yes-user-uef @@ -2790,6 +2792,7 @@ make machine :pre [Supporting info:] src/USER-UEF: filenames -> commands +src/USER-UEF/README "fix nvt/uef"_fix_nh_uef.html "compute pressure/uef"_compute_pressure_uef.html "compute temp/uef"_compute_temp_uef.html diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt new file mode 100644 index 0000000000..e2e49da26d --- /dev/null +++ b/doc/src/compute_pressure_uef.txt @@ -0,0 +1,61 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute pressure/uef command :h3 + +[Syntax:] + +compute ID group-ID pressure/uef temp-ID keyword ... :pre + +ID, group-ID are documented in "compute"_compute.html command +pressure = style name of this compute command +temp-ID = ID of compute that calculates temperature, can be NULL if not needed +zero or more keywords may be appended +keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul + +[Examples:] + +compute 1 all pressure/uef my_temp_uef +compute 2 all pressure/uef my_temp_uef virial :pre + +[Description:] + +This command is used to compute the pressure tensor in +the reference frame of the applied flow field when +"fix nvt/uef"_fix_nh_uef.html" or +"fix npt/uef"_fix_nh_uef.html" is used. +It is not necessary to use this command to compute the scalar +value of the pressure. A "compute pressure"_compute_pressure.html +may be used for that purpose. + +The keywords and output information are documented in +"compute_pressure"_compute_pressure.html. + +[Restrictions:] + +This fix is part of the USER-UEF package. It is only enabled if +LAMMPS was built with that package. See the +"Making LAMMPS"_Section_start.html#start_3 section for more info. + +This command can only be used when "fix nvt/uef"_fix_nh_uef.html +or "fix npt/uef"_fix_nh_uef.html is active. + +The kinetic contribution to the pressure tensor +will be accurate only when +the compute specificed by {temp-ID} is a +"compute temp/uef"_compute_temp_uef.html. + +[Related commands:] + +"compute pressure"_compute_pressure.html, +"fix nvt/uef"_fix_nh_uef.html, +"compute temp/uef"_compute_temp_uef.html + +[Default:] none + + diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt index 33f847af35..562ad89b66 100644 --- a/doc/src/compute_temp_uef.txt +++ b/doc/src/compute_temp_uef.txt @@ -6,30 +6,30 @@ :line -compute temp command :h3 -compute temp/kk command :h3 +compute temp/uef command :h3 [Syntax:] -compute ID group-ID temp :pre +compute ID group-ID temp/uef :pre ID, group-ID are documented in "compute"_compute.html command temp = style name of this compute command :ul [Examples:] -compute 1 all temp/uef +compute 1 all temp/uef +compute 2 sel temp/uef :pre [Description:] This command is used to compute the kinetic energy tensor in -the correct reference frame when the USER-UEF package is used. +the reference frame of the applied flow field when +"fix nvt/uef"_fix_nh_uef.html" or +"fix npt/uef"_fix_nh_uef.html" is used. It is not necessary to use this command to compute the scalar value of the temperature. A "compute temp"_compute_temp.html may be used for that purpose. -[Output info:] - Output information for this command can be found in the documentation for "compute temp"_compute_temp.html. @@ -37,13 +37,13 @@ documentation for "compute temp"_compute_temp.html. This fix is part of the USER-UEF package. It is only enabled if LAMMPS was built with that package. See the -"Making LAMMPS"_Section_start.html#start-3 section for more info. - +"Making LAMMPS"_Section_start.html#start_3 section for more info. This command can only be used when "fix nvt/uef"_fix_nh_uef.html or "fix npt/uef"_fix_nh_uef.html is active. [Related commands:] + "compute temp"_compute_temp.html, "fix nvt/uef"_fix_nh_uef.html, "compute pressure/uef"_compute_pressure_uef.html diff --git a/doc/src/computes.txt b/doc/src/computes.txt index c443bfaba2..1b64e2e5b4 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -65,6 +65,7 @@ Computes :h1 compute_pe_atom compute_plasticity_atom compute_pressure + compute_pressure_uef compute_property_atom compute_property_chunk compute_property_local @@ -114,6 +115,7 @@ Computes :h1 compute_temp_region_eff compute_temp_rotate compute_temp_sphere + compute_temp_uef compute_ti compute_torque_chunk compute_vacf diff --git a/doc/src/dump_cfg_uef.txt b/doc/src/dump_cfg_uef.txt index a857ea4820..e257f9c4f1 100644 --- a/doc/src/dump_cfg_uef.txt +++ b/doc/src/dump_cfg_uef.txt @@ -23,7 +23,7 @@ args = same as args for "dump custom"_dump.html :pre [Examples:] dump 1 all cfg/uef 10 dump.*.cfg mass type xs ys zs -dump 2 all cfg/uef 100 dump.*.cfg mass type xs ys zs id c_stress +dump 2 all cfg/uef 100 dump.*.cfg mass type xs ys zs id c_stress :pre [Description:] diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt index 38d01edccf..250d5624d0 100644 --- a/doc/src/fix_nh_uef.txt +++ b/doc/src/fix_nh_uef.txt @@ -15,15 +15,15 @@ fix ID group-ID style_name erate eps_x eps_y temp Tstart Tstop Tdamp keyword val ID, group-ID are documented in "fix"_fix.html command :ulb,l style_name = {nvt/uef} or {npt/uef} :l -Tstart, Tstop, and Tdamp are documented in the "fix_npt"_fix_nh.html command :l -edot_x and edot_y are the strain rates in the x and y directions (1/(time units)) :l +{Tstart}, {Tstop}, and {Tdamp} are documented in the "fix npt"_fix_nh.html command :l +{edot_x} and {edot_y} are the strain rates in the x and y directions (1/(time units)) :l one or more keyword/value pairs may be appended :l keyword = {ext} or {strain} or {iso} or {x} or {y} or {z} or {tchain} or {pchain} or {tloop} or {ploop} or {mtk} {ext} value = {x} or {y} or {z} or {xy} or {yz} or {xz} = external dimensions This keyword sets the external dimensions used to calculate the scalar pressure {strain} values = e_x e_y = initial strain Use of this keyword is usually not necessary, but may be needed to resume a run with a data file. - The {iso}, {x}, {y}, {z}, {tchain}, {pchain}, {tloop}, {ploop}, and {mtk} keywords are documented in the "fix_npt"_fix_nh.html command. :pre + The {iso}, {x}, {y}, {z}, {tchain}, {pchain}, {tloop}, {ploop}, and {mtk} keywords are documented in the "fix npt"_fix_nh.html command. :pre :ule [Examples:] @@ -46,8 +46,13 @@ as was proposed by "(Hunt)"_#Hunt. The lattice reduction algorithm is from homogeneous flows, and integrates the SLLOD equations of motion, originally proposed by Hoover and Ladd (see "(Evans and Morriss)"_#Sllod). +The applied flow field is set by the {eps} keyword. The values {edot_x} +and {edot_y} correspond to the strain rates in the xx and yy directions. +It is implicitly assumed that the flow field is traceless, and therefore +the strain rate in the zz direction is eqal to -({edot_x} + {edot_y}). + NOTE: Due to an instability in the SLLOD equations under extension, -"fix_momentum"_fix_momentum.html should be used to regularly reset the +"fix momentum"_fix_momentum.html should be used to regularly reset the linear momentum. The boundary conditions require a simulation box that does not have a @@ -58,47 +63,49 @@ This fix keeps track of two coordinate systems: the flow frame, and the upper triangular LAMMPS frame. The coordinate systems are related to each other through the QR decomposition, as is illustrated in the image below. -image +:c,image(JPG/uef_frames.jpg) During most molecular dynamics operations, the system is represented in the LAMMPS frame. Only when the positions and velocities are updated is the system rotated to the flow frame, and it is rotated back to the LAMMPS frame immediately afterwards. For this reason, all vector-valued quantities -(except for the tensors from compute pressure/uef and compute temp/uef) will +(except for the tensors from "compute_pressure/uef"_compute_pressure_uef.html +and "compute_temp/uef"_compute_temp_uef.html) will be computed in the LAMMPS frame. Rotationally invariant scalar quantities like -the temperature and hydrostatic pressure, on the other hand, will be computed -correctly. Additionally, the system is in the LAMMPS frame during all of the +the temperature and hydrostatic pressure are frame-invariant and will be +computed correctly. Additionally, the system is in the LAMMPS frame during all of the output steps, and therefore trajectory files made using the dump command -will be in the LAMMPS frame unless the dump cfg/uef command is used. +will be in the LAMMPS frame unless the "dump_cfg/uef"_dump_cfg_uef.html command is used. :line Temperature control is achieved with the default Nose-Hoover style -thermostat documented in "fix_npt"_fix_nh.html. When this fix is active, +thermostat documented in "fix npt"_fix_nh.html. When this fix is active, only the peculiar velocity of each atom is stored, defined as the velocity relative to the streaming velocity. This is in contrast to -"fix_nvt/sllod"_fix_nvt_sllod.html, which uses a lab-frame velocity, and +"fix nvt/sllod"_fix_nvt_sllod.html, which uses a lab-frame velocity, and removes the contribution from the streaming velocity in order to compute the temperature. Pressure control is achieved using the default Nose-Hoover barostat documented -in "fix_npt"_fix_npt.html. There are two ways to control the pressure using this +in "fix npt"_fix_nh.html. There are two ways to control the pressure using this fix. The first method involves using the {ext} keyword along with the {iso} pressure style. With this method, the pressure is controlled by scaling the simulation box -isotropically to achieve the average pressure in the directions specified by {ext}. -For example, if {ext xy} is used, the average pressure (Pxx+Pyy)/2 will be controlled. +isotropically to achieve the average pressure only in the directions specified by {ext}. +For example, if the {ext} values is set to {xy}, the average pressure (Pxx+Pyy)/2 +will be controlled. -This command will control the total hydrostatic pressure under uniaxial tension: +This example command will control the total hydrostatic pressure under uniaxial tension: fix f1 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xyz :pre -This command will control the average stress in compression directions, which would -correspond to free surfaces for fiber drawing, under uniaxial tension: +This example command will control the average stress in compression directions, which would +typically correspond to free surfaces under drawing with uniaxial tension: fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy :pre The second method for pressure control involves setting the normal stresses using -the x, y , and/or z keywords. When using this method, the same pressure must be +the {x}, {y} , and/or {z} keywords. When using this method, the same pressure must be specified via {Pstart} and {Pstop} for all dimensions controlled. Any choice of pressure conditions that would cause LAMMPS to compute a deviatoric stress are not permissible and will result in an error. Additionally, all dimensions with @@ -117,19 +124,74 @@ fix f6 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 2 2 5 erate 0.5 0.5 :pre :line +These fix computes a temperature and pressure each timestep. To do +this, it creates its own computes of style "temp/uef" and "pressure/uef", +as if one of these two sets of commands had been issued: + +compute fix-ID_temp group-ID temp/uef +compute fix-ID_press group-ID pressure/uef fix-ID_temp :pre + +compute fix-ID_temp all temp/uef +compute fix-ID_press all pressure/uef fix-ID_temp :pre + +See the "compute temp/uef"_compute_temp_uef.html and "compute +pressure/uef"_compute_pressure_uef.html commands for details. Note that the +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID ++ underscore + "press". + +[Restart, fix_modify, output, run start/stop, minimize info:] + +The fix writes the state of all the thermostat and barostat +variables, as well as the cumulative strain applied, to +"binary restart files"_restart.html. See the +"read_restart"_read_restart.html command for info on how to re-specify +a fix in an input script that reads a restart file, so that the +operation of the fix continues in an uninterrupted fashion. + +NOTE: It is not necessary to set the {strain} keyword when resuming +a run from a restart file. Only for resuming from data files, +which do not contain the cumulative applied strain, will +this keyword be necessary. + +This fix can be used with the "fix_modify"_fix_modify.html +{temp} and {press} options. The temperature and pressure computes +used must be of type {temp/uef} and {pressure/uef}. + +This fix computes the same global scalar and vecor quantities +as "fix npt"_fix_nh.html. + +The fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] -Due to requirements of the boundary conditions, when the strain keyword -is unset, or set to zero, the initial simulation box must be cubic and +This fix is part of the USER-UEF package. It is only enabled if +LAMMPS was built with that package. See the +"Making LAMMPS"_Section_start.html#start_3 section for more info. + +Due to requirements of the boundary conditions, when the {strain} keyword +is set to zero (or unset), the initial simulation box must be cubic and have style triclinic. If the box is initially of type ortho, use "change_box"_change_box.html before invoking the fix. -When this fix is applied, any orientation-dependent vector or -tensor-valued quantities computed, except for the tensors from -compute pressure/uef/compute temp/uef and coordinates from -dump cfg/uef, will not be in the same coordinate system as -the flow field. +NOTE: When resuming from restart files, you may need to use "box tilt large"_box.html +since lammps has internal criteria from lattice reduction that are not +the same as the criteria in the numerical lattice reduction algorithm. + +[Related commands:] +"fix nvt"_fix_nh.html, +"fix nvt/sllod"_fix_nvt_sllod.html, +"compute temp/uef"_compute_temp_uef.html, +"compute pressure/uef"_compute_pressure_uef.html, +"dump cfg/uef"_dump_cfg_uef.html + +[Default:] + +The default keyword values specific to this fix are exy = xyz, strain = 0 0. +The remaining defaults are the same as for {fix npt}_fix_nh.html except tchain = 1. +The reason for this change is given in "fix nvt/sllod"_fix_nvt_sllod.html. + +:line :link(Dobson) [(Dobson)] Dobson, J Chem Phys, 141, 184103 (2014). @@ -142,574 +204,3 @@ the flow field. :link(Sllod) [(Evans and Morriss)] Evans and Morriss, Phys Rev A, 30, 1528 (1984). - -These commands perform time integration on Nose-Hoover style -non-Hamiltonian equations of motion which are designed to generate -positions and velocities sampled from the canonical (nvt), -isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This -updates the position and velocity for atoms in the group each -timestep. - -The thermostatting and barostatting is achieved by adding some dynamic -variables which are coupled to the particle velocities -(thermostatting) and simulation domain dimensions (barostatting). In -addition to basic thermostatting and barostatting, these fixes can -also create a chain of thermostats coupled to the particle thermostat, -and another chain of thermostats coupled to the barostat -variables. The barostat can be coupled to the overall box volume, or -to individual dimensions, including the {xy}, {xz} and {yz} tilt -dimensions. The external pressure of the barostat can be specified as -either a scalar pressure (isobaric ensemble) or as components of a -symmetric stress tensor (constant stress ensemble). When used -correctly, the time-averaged temperature and stress tensor of the -particles will match the target values specified by Tstart/Tstop and -Pstart/Pstop. - -The equations of motion used are those of Shinoda et al in -"(Shinoda)"_#nh-Shinoda, which combine the hydrostatic equations of -Martyna, Tobias and Klein in "(Martyna)"_#nh-Martyna with the strain -energy proposed by Parrinello and Rahman in -"(Parrinello)"_#nh-Parrinello. The time integration schemes closely -follow the time-reversible measure-preserving Verlet and rRESPA -integrators derived by Tuckerman et al in "(Tuckerman)"_#nh-Tuckerman. - -:line - -The thermostat parameters for fix styles {nvt} and {npt} is specified -using the {temp} keyword. Other thermostat-related keywords are -{tchain}, {tloop} and {drag}, which are discussed below. - -The thermostat is applied to only the translational degrees of freedom -for the particles. The translational degrees of freedom can also have -a bias velocity removed before thermostatting takes place; see the -description below. The desired temperature at each timestep is a -ramped value during the run from {Tstart} to {Tstop}. The {Tdamp} -parameter is specified in time units and determines how rapidly the -temperature is relaxed. For example, a value of 10.0 means to relax -the temperature in a timespan of (roughly) 10 time units (e.g. tau or -fmsec or psec - see the "units"_units.html command). The atoms in the -fix group are the only ones whose velocities and positions are updated -by the velocity/position update portion of the integration. - -NOTE: A Nose-Hoover thermostat will not work well for arbitrary values -of {Tdamp}. If {Tdamp} is too small, the temperature can fluctuate -wildly; if it is too large, the temperature will take a very long time -to equilibrate. A good choice for many models is a {Tdamp} of around -100 timesteps. Note that this is NOT the same as 100 time units for -most "units"_units.html settings. - -:line - -The barostat parameters for fix styles {npt} and {nph} is specified -using one or more of the {iso}, {aniso}, {tri}, {x}, {y}, {z}, {xy}, -{xz}, {yz}, and {couple} keywords. These keywords give you the -ability to specify all 6 components of an external stress tensor, and -to couple various of these components together so that the dimensions -they represent are varied together during a constant-pressure -simulation. - -Other barostat-related keywords are {pchain}, {mtk}, {ploop}, -{nreset}, {drag}, and {dilate}, which are discussed below. - -Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). -Triclinic (non-orthogonal) simulation boxes have 6 adjustable -dimensions (x,y,z,xy,xz,yz). The "create_box"_create_box.html, "read -data"_read_data.html, and "read_restart"_read_restart.html commands -specify whether the simulation box is orthogonal or non-orthogonal -(triclinic) and explain the meaning of the xy,xz,yz tilt factors. - -The target pressures for each of the 6 components of the stress tensor -can be specified independently via the {x}, {y}, {z}, {xy}, {xz}, {yz} -keywords, which correspond to the 6 simulation box dimensions. For -each component, the external pressure or tensor component at each -timestep is a ramped value during the run from {Pstart} to {Pstop}. -If a target pressure is specified for a component, then the -corresponding box dimension will change during a simulation. For -example, if the {y} keyword is used, the y-box length will change. If -the {xy} keyword is used, the xy tilt factor will change. A box -dimension will not change if that component is not specified, although -you have the option to change that dimension via the "fix -deform"_fix_deform.html command. - -Note that in order to use the {xy}, {xz}, or {yz} keywords, the -simulation box must be triclinic, even if its initial tilt factors are -0.0. - -For all barostat keywords, the {Pdamp} parameter operates like the -{Tdamp} parameter, determining the time scale on which pressure is -relaxed. For example, a value of 10.0 means to relax the pressure in -a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see -the "units"_units.html command). - -NOTE: A Nose-Hoover barostat will not work well for arbitrary values -of {Pdamp}. If {Pdamp} is too small, the pressure and volume can -fluctuate wildly; if it is too large, the pressure will take a very -long time to equilibrate. A good choice for many models is a {Pdamp} -of around 1000 timesteps. However, note that {Pdamp} is specified in -time units, and that timesteps are NOT the same as time units for most -"units"_units.html settings. - -Regardless of what atoms are in the fix group (the only atoms which -are time integrated), a global pressure or stress tensor is computed -for all atoms. Similarly, when the size of the simulation box is -changed, all atoms are re-scaled to new positions, unless the keyword -{dilate} is specified with a {dilate-group-ID} for a group that -represents a subset of the atoms. This can be useful, for example, to -leave the coordinates of atoms in a solid substrate unchanged and -controlling the pressure of a surrounding fluid. This option should -be used with care, since it can be unphysical to dilate some atoms and -not others, because it can introduce large, instantaneous -displacements between a pair of atoms (one dilated, one not) that are -far from the dilation origin. Also note that for atoms not in the fix -group, a separate time integration fix like "fix nve"_fix_nve.html or -"fix nvt"_fix_nh.html can be used on them, independent of whether they -are dilated or not. - -:line - -The {couple} keyword allows two or three of the diagonal components of -the pressure tensor to be "coupled" together. The value specified -with the keyword determines which are coupled. For example, {xz} -means the {Pxx} and {Pzz} components of the stress tensor are coupled. -{Xyz} means all 3 diagonal components are coupled. Coupling means two -things: the instantaneous stress will be computed as an average of the -corresponding diagonal components, and the coupled box dimensions will -be changed together in lockstep, meaning coupled dimensions will be -dilated or contracted by the same percentage every timestep. The -{Pstart}, {Pstop}, {Pdamp} parameters for any coupled dimensions must -be identical. {Couple xyz} can be used for a 2d simulation; the {z} -dimension is simply ignored. - -:line - -The {iso}, {aniso}, and {tri} keywords are simply shortcuts that are -equivalent to specifying several other keywords together. - -The keyword {iso} means couple all 3 diagonal components together when -pressure is computed (hydrostatic pressure), and dilate/contract the -dimensions together. Using "iso Pstart Pstop Pdamp" is the same as -specifying these 4 keywords: - -x Pstart Pstop Pdamp -y Pstart Pstop Pdamp -z Pstart Pstop Pdamp -couple xyz :pre - -The keyword {aniso} means {x}, {y}, and {z} dimensions are controlled -independently using the {Pxx}, {Pyy}, and {Pzz} components of the -stress tensor as the driving forces, and the specified scalar external -pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying -these 4 keywords: - -x Pstart Pstop Pdamp -y Pstart Pstop Pdamp -z Pstart Pstop Pdamp -couple none :pre - -The keyword {tri} means {x}, {y}, {z}, {xy}, {xz}, and {yz} dimensions -are controlled independently using their individual stress components -as the driving forces, and the specified scalar pressure as the -external normal stress. Using "tri Pstart Pstop Pdamp" is the same as -specifying these 7 keywords: - -x Pstart Pstop Pdamp -y Pstart Pstop Pdamp -z Pstart Pstop Pdamp -xy 0.0 0.0 Pdamp -yz 0.0 0.0 Pdamp -xz 0.0 0.0 Pdamp -couple none :pre - -:line - -In some cases (e.g. for solids) the pressure (volume) and/or -temperature of the system can oscillate undesirably when a Nose/Hoover -barostat and thermostat is applied. The optional {drag} keyword will -damp these oscillations, although it alters the Nose/Hoover equations. -A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged. -A non-zero value adds a drag term; the larger the value specified, the -greater the damping effect. Performing a short run and monitoring the -pressure and temperature is the best way to determine if the drag term -is working. Typically a value between 0.2 to 2.0 is sufficient to -damp oscillations after a few periods. Note that use of the drag -keyword will interfere with energy conservation and will also change -the distribution of positions and velocities so that they do not -correspond to the nominal NVT, NPT, or NPH ensembles. - -An alternative way to control initial oscillations is to use chain -thermostats. The keyword {tchain} determines the number of thermostats -in the particle thermostat. A value of 1 corresponds to the original -Nose-Hoover thermostat. The keyword {pchain} specifies the number of -thermostats in the chain thermostatting the barostat degrees of -freedom. A value of 0 corresponds to no thermostatting of the -barostat variables. - -The {mtk} keyword controls whether or not the correction terms due to -Martyna, Tuckerman, and Klein are included in the equations of motion -"(Martyna)"_#nh-Martyna. Specifying {no} reproduces the original -Hoover barostat, whose volume probability distribution function -differs from the true NPT and NPH ensembles by a factor of 1/V. Hence -using {yes} is more correct, but in many cases the difference is -negligible. - -The keyword {tloop} can be used to improve the accuracy of integration -scheme at little extra cost. The initial and final updates of the -thermostat variables are broken up into {tloop} substeps, each of -length {dt}/{tloop}. This corresponds to using a first-order -Suzuki-Yoshida scheme "(Tuckerman)"_#nh-Tuckerman. The keyword {ploop} -does the same thing for the barostat thermostat. - -The keyword {nreset} controls how often the reference dimensions used -to define the strain energy are reset. If this keyword is not used, -or is given a value of zero, then the reference dimensions are set to -those of the initial simulation domain and are never changed. If the -simulation domain changes significantly during the simulation, then -the final average pressure tensor will differ significantly from the -specified values of the external stress tensor. A value of {nstep} -means that every {nstep} timesteps, the reference dimensions are set -to those of the current simulation domain. - -The {scaleyz}, {scalexz}, and {scalexy} keywords control whether or -not the corresponding tilt factors are scaled with the associated box -dimensions when barostatting triclinic periodic cells. The default -values {yes} will turn on scaling, which corresponds to adjusting the -linear dimensions of the cell while preserving its shape. Choosing -{no} ensures that the tilt factors are not scaled with the box -dimensions. See below for restrictions and default values in different -situations. In older versions of LAMMPS, scaling of tilt factors was -not performed. The old behavior can be recovered by setting all three -scale keywords to {no}. - -The {flip} keyword allows the tilt factors for a triclinic box to -exceed half the distance of the parallel box length, as discussed -below. If the {flip} value is set to {yes}, the bound is enforced by -flipping the box when it is exceeded. If the {flip} value is set to -{no}, the tilt will continue to change without flipping. Note that if -applied stress induces large deformations (e.g. in a liquid), this -means the box shape can tilt dramatically and LAMMPS will run less -efficiently, due to the large volume of communication needed to -acquire ghost atoms around a processor's irregular-shaped sub-domain. -For extreme values of tilt, LAMMPS may also lose atoms and generate an -error. - -The {fixedpoint} keyword specifies the fixed point for barostat volume -changes. By default, it is the center of the box. Whatever point is -chosen will not move during the simulation. For example, if the lower -periodic boundaries pass through (0,0,0), and this point is provided -to {fixedpoint}, then the lower periodic boundaries will remain at -(0,0,0), while the upper periodic boundaries will move twice as -far. In all cases, the particle trajectories are unaffected by the -chosen value, except for a time-dependent constant translation of -positions. - -If the {update} keyword is used with the {dipole} value, then the -orientation of the dipole moment of each particle is also updated -during the time integration. This option should be used for models -where a dipole moment is assigned to finite-size particles, -e.g. spheroids via use of the "atom_style hybrid sphere -dipole"_atom_style.html command. - -The default dipole orientation integrator can be changed to the -Dullweber-Leimkuhler-McLachlan integration scheme -"(Dullweber)"_#nh-Dullweber when using {update} with the value -{dipole/dlm}. This integrator is symplectic and time-reversible, -giving better energy conservation and allows slightly longer timesteps -at only a small additional computational cost. - -:line - -NOTE: Using a barostat coupled to tilt dimensions {xy}, {xz}, {yz} can -sometimes result in arbitrarily large values of the tilt dimensions, -i.e. a dramatically deformed simulation box. LAMMPS allows the tilt -factors to grow a small amount beyond the normal limit of half the box -length (0.6 times the box length), and then performs a box "flip" to -an equivalent periodic cell. See the discussion of the {flip} keyword -above, to allow this bound to be exceeded, if desired. - -The flip operation is described in more detail in the doc page for -"fix deform"_fix_deform.html. Both the barostat dynamics and the atom -trajectories are unaffected by this operation. However, if a tilt -factor is incremented by a large amount (1.5 times the box length) on -a single timestep, LAMMPS can not accomodate this event and will -terminate the simulation with an error. This error typically indicates -that there is something badly wrong with how the simulation was -constructed, such as specifying values of {Pstart} that are too far -from the current stress value, or specifying a timestep that is too -large. Triclinic barostatting should be used with care. This also is -true for other barostat styles, although they tend to be more -forgiving of insults. In particular, it is important to recognize that -equilibrium liquids can not support a shear stress and that -equilibrium solids can not support shear stresses that exceed the -yield stress. - -One exception to this rule is if the 1st dimension in the tilt factor -(x for xy) is non-periodic. In that case, the limits on the tilt -factor are not enforced, since flipping the box in that dimension does -not change the atom positions due to non-periodicity. In this mode, -if you tilt the system to extreme angles, the simulation will simply -become inefficient due to the highly skewed simulation box. - -NOTE: Unlike the "fix temp/berendsen"_fix_temp_berendsen.html command -which performs thermostatting but NO time integration, these fixes -perform thermostatting/barostatting AND time integration. Thus you -should not use any other time integration fix, such as "fix -nve"_fix_nve.html on atoms to which this fix is applied. Likewise, -fix nvt and fix npt should not normally be used on atoms that also -have their temperature controlled by another fix - e.g. by "fix -langevin"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html -commands. - -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform -thermostatting and barostatting. - -:line - -These fixes compute a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp" and "pressure", -as if one of these two sets of commands had been issued: - -compute fix-ID_temp group-ID temp -compute fix-ID_press group-ID pressure fix-ID_temp :pre - -compute fix-ID_temp all temp -compute fix-ID_press all pressure fix-ID_temp :pre - -See the "compute temp"_compute_temp.html and "compute -pressure"_compute_pressure.html commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press". For fix nvt, the group for the new computes -is the same as the fix group. For fix nph and fix npt, the group for -the new computes is "all" since pressure is computed for the entire -system. - -Note that these are NOT the computes used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} -and {thermo_press}. This means you can change the attributes of this -fix's temperature or pressure via the -"compute_modify"_compute_modify.html command or print this temperature -or pressure during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} or -{thermo_press} will have no effect on this fix. - -Like other fixes that perform thermostatting, fix nvt and fix npt can -be used with "compute commands"_compute.html that calculate a -temperature after removing a "bias" from the atom velocities. -E.g. removing the center-of-mass velocity from a group of atoms or -only calculating temperature on the x-component of velocity or only -calculating temperature for atoms in a geometric region. This is not -done by default, but only if the "fix_modify"_fix_modify.html command -is used to assign a temperature compute to this fix that includes such -a bias term. See the doc pages for individual "compute -commands"_compute.html to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. - -:line - -These fixes can be used with either the {verlet} or {respa} -"integrators"_run_style.html. When using one of the barostat fixes -with {respa}, LAMMPS uses an integrator constructed -according to the following factorization of the Liouville propagator -(for two rRESPA levels): - -:c,image(Eqs/fix_nh1.jpg) - -This factorization differs somewhat from that of Tuckerman et al, in -that the barostat is only updated at the outermost rRESPA level, -whereas Tuckerman's factorization requires splitting the pressure into -pieces corresponding to the forces computed at each rRESPA level. In -theory, the latter method will exhibit better numerical stability. In -practice, because Pdamp is normally chosen to be a large multiple of -the outermost rRESPA timestep, the barostat dynamics are not the -limiting factor for numerical stability. Both factorizations are -time-reversible and can be shown to preserve the phase space measure -of the underlying non-Hamiltonian equations of motion. - -NOTE: This implementation has been shown to conserve linear momentum -up to machine precision under NVT dynamics. Under NPT dynamics, -for a system with zero initial total linear momentum, the total -momentum fluctuates close to zero. It may occasionally undergo brief -excursions to non-negligible values, before returning close to zero. -Over long simulations, this has the effect of causing the center-of-mass -to undergo a slow random walk. This can be mitigated by resetting -the momentum at infrequent intervals using the -"fix momentum"_fix_momentum.html command. - -:line - -The fix npt and fix nph commands can be used with rigid bodies or -mixtures of rigid bodies and non-rigid particles (e.g. solvent). But -there are also "fix rigid/npt"_fix_rigid.html and "fix -rigid/nph"_fix_rigid.html commands, which are typically a more natural -choice. See the doc page for those commands for more discussion of -the various ways to do this. - -:line - -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 in "Section 5"_Section_accelerate.html -of the manual. 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 "Making -LAMMPS"_Section_start.html#start_3 section for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. - -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -These fixes writes the state of all the thermostat and barostat -variables to "binary restart files"_restart.html. See the -"read_restart"_read_restart.html command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. - -The "fix_modify"_fix_modify.html {temp} and {press} options are -supported by these fixes. You can use them to assign a -"compute"_compute.html you have defined to this fix which will be used -in its thermostatting or barostatting procedure, as described above. -If you do this, note that the kinetic energy derived from the compute -temperature should be consistent with the virial term computed using -all atoms for the pressure. LAMMPS will warn you if you choose to -compute temperature on a subset of atoms. - -NOTE: If both the {temp} and {press} keywords are used in a single -thermo_modify command (or in two separate commands), then the order in -which the keywords are specified is important. Note that a "pressure -compute"_compute_pressure.html defines its own temperature compute as -an argument when it is specified. The {temp} keyword will override -this (for the pressure compute being used by fix npt), but only if the -{temp} keyword comes after the {press} keyword. If the {temp} keyword -comes before the {press} keyword, then the new pressure compute -specified by the {press} keyword will be unaffected by the {temp} -setting. - -The "fix_modify"_fix_modify.html {energy} option is supported by these -fixes to add the energy change induced by Nose/Hoover thermostatting -and barostatting to the system's potential energy as part of -"thermodynamic output"_thermo_style.html. - -These fixes compute a global scalar and a global vector of quantities, -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar value calculated by -these fixes is "extensive"; the vector values are "intensive". - -The scalar is the cumulative energy change due to the fix. - -The vector stores internal Nose/Hoover thermostat and barostat -variables. The number and meaning of the vector values depends on -which fix is used and the settings for keywords {tchain} and {pchain}, -which specify the number of Nose/Hoover chains for the thermostat and -barostat. If no thermostatting is done, then {tchain} is 0. If no -barostatting is done, then {pchain} is 0. In the following list, -"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in -the barostat. Its value is 0 if no barostat is used, else its value -is 6 if any off-diagonal stress tensor component is barostatted, else -its value is 1 if {couple xyz} is used or {couple xy} for a 2d -simulation, otherwise its value is 3. - -The order of values in the global vector and their meaning is as -follows. The notation means there are tchain values for eta, followed -by tchain for eta_dot, followed by ndof for omega, etc: - -eta\[tchain\] = particle thermostat displacements (unitless) -eta_dot\[tchain\] = particle thermostat velocities (1/time units) -omega\[ndof\] = barostat displacements (unitless) -omega_dot\[ndof\] = barostat velocities (1/time units) -etap\[pchain\] = barostat thermostat displacements (unitless) -etap_dot\[pchain\] = barostat thermostat velocities (1/time units) -PE_eta\[tchain\] = potential energy of each particle thermostat displacement (energy units) -KE_eta_dot\[tchain\] = kinetic energy of each particle thermostat velocity (energy units) -PE_omega\[ndof\] = potential energy of each barostat displacement (energy units) -KE_omega_dot\[ndof\] = kinetic energy of each barostat velocity (energy units) -PE_etap\[pchain\] = potential energy of each barostat thermostat displacement (energy units) -KE_etap_dot\[pchain\] = kinetic energy of each barostat thermostat velocity (energy units) -PE_strain\[1\] = scalar strain energy (energy units) :ul - -These fixes can ramp their external temperature and pressure over -multiple runs, using the {start} and {stop} keywords of the -"run"_run.html command. See the "run"_run.html command for details of -how to do this. - -These fixes are not invoked during "energy -minimization"_minimize.html. - -:line - -[Restrictions:] - -{X}, {y}, {z} cannot be barostatted if the associated dimension is not -periodic. {Xy}, {xz}, and {yz} can only be barostatted if the -simulation domain is triclinic and the 2nd dimension in the keyword -({y} dimension in {xy}) is periodic. {Z}, {xz}, and {yz}, cannot be -barostatted for 2D simulations. The "create_box"_create_box.html, -"read data"_read_data.html, and "read_restart"_read_restart.html -commands specify whether the simulation box is orthogonal or -non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz -tilt factors. - -For the {temp} keyword, the final Tstop cannot be 0.0 since it would -make the external T = 0.0 at some timestep during the simulation which -is not allowed in the Nose/Hoover formulation. - -The {scaleyz yes} and {scalexz yes} keyword/value pairs can not be used -for 2D simulations. {scaleyz yes}, {scalexz yes}, and {scalexy yes} options -can only be used if the 2nd dimension in the keyword is periodic, -and if the tilt factor is not coupled to the barostat via keywords -{tri}, {yz}, {xz}, and {xy}. - -These fixes can be used with dynamic groups as defined by the -"group"_group.html command. Likewise they can be used with groups to -which atoms are added or deleted over time, e.g. a deposition -simulation. However, the conservation properties of the thermostat -and barostat are defined for systems with a static set of atoms. You -may observe odd behavior if the atoms in a group vary dramatically -over time or the atom count becomes very small. - -[Related commands:] - -"fix nve"_fix_nve.html, "fix_modify"_fix_modify.html, -"run_style"_run_style.html - -[Default:] - -The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = -ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none, -scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and -not coupled to barostat, otherwise no. - -:line - -:link(nh-Martyna) -[(Martyna)] Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). - -:link(nh-Parrinello) -[(Parrinello)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). - -:link(nh-Tuckerman) -[(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and -Martyna, J Phys A: Math Gen, 39, 5629 (2006). - -:link(nh-Shinoda) -[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). - -:link(nh-Dullweber) -[(Dullweber)] Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, -5840 (1997). diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index 7000a66c51..b93bb9d0a2 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -76,6 +76,7 @@ Fixes :h1 fix_neb fix_nh fix_nh_eff + fix_nh_uef fix_nph_asphere fix_nph_body fix_nph_sphere From 480b087c9392de42fda2e67b5589b12613a5a5a8 Mon Sep 17 00:00:00 2001 From: David Nicholson Date: Thu, 28 Sep 2017 18:31:51 -0400 Subject: [PATCH 05/21] doc edits, README, and citeme --- doc/src/Section_packages.txt | 1 + src/USER-UEF/README | 47 ++++++++++++++++++++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 src/USER-UEF/README diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index 58e41fc4ed..6451581d3a 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -2794,6 +2794,7 @@ make machine :pre src/USER-UEF: filenames -> commands src/USER-UEF/README "fix nvt/uef"_fix_nh_uef.html +"fix npt/uef"_fix_nh_uef.html "compute pressure/uef"_compute_pressure_uef.html "compute temp/uef"_compute_temp_uef.html "dump cfg/uef"_dump_cfg_uef.html diff --git a/src/USER-UEF/README b/src/USER-UEF/README new file mode 100644 index 0000000000..92b2cee5e3 --- /dev/null +++ b/src/USER-UEF/README @@ -0,0 +1,47 @@ +USER-UEF is a LAMMPS package for non-equilibrium molecular dynamics +(NEMD) under diagonal flow fields, including uniaxial and biaxial +flow. With this package, simulations under extensional flow may be +carried out for an indefinite amount of time. It is an implementation +of the boundary conditions developed by Matthew Dobson, and also uses +numerical lattice reduction as was proposed by Thomas Hunt. The +lattice reduction algorithm is from Igor Semaev. The package is +intended for simulations of homogeneous flows, and integrates the +SLLOD equations of motion. + +-- + +This package was created by David Nicholson (davidanich@gmail.com) +at the Massachusetts Institute of Technology. + +-- + +The following commands are contained in this package: + +fix npt/uef and fix nvt/uef: + These commands perform time-integration of the SLLOD equations of + motion under constant temperature/pressure with the proper + boundary conditions for extensional flow fields. + +compute pressure/uef and compute temp/uef: + These commands allow for the evaluation of pressure/ke tensors in + the reference frame corresponding to the applied flow field. + +dump cfg/uef: + This command dumps coordinates in the reference frame corresponding + to the applied flow field. + +For more information, visit the documentation page for fix nvt/uef +and examine the example scripts in doc/USER/uef/. + +-- + +References: + +I. Semaev, Cryptography and Lattices, 181 (2001). + +M. Dobson, J. Chem. Phys., 141, 184103 (2014) + +T.A. Hunt, Mol. Simul., 42, 347 (2016). + +D.A. Nicholson, G.C. Rutledge, J. Chem. Phys.,145, 244903 (2016) + From a64040ce2d4fb0e5a4a11a5750c4069e0061ebfc Mon Sep 17 00:00:00 2001 From: David Nicholson Date: Thu, 28 Sep 2017 18:33:04 -0400 Subject: [PATCH 06/21] citeme --- src/USER-UEF/fix_nh_uef.cpp | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp index 74d4e78746..1bc9386ad6 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -21,6 +21,7 @@ #include "force.h" #include "group.h" #include "comm.h" +#include "citeme.h" #include "irregular.h" #include "modify.h" #include "compute.h" @@ -95,6 +96,19 @@ char ** FixNHUef::arg_kludge(int &narg, char **arg, int &rem) return arg; } +//citation info +static const char cite_user_uef_package[] = + "USER-UEF package:\n\n" + "@Article{NicholsonRutledge16,\n" + "author = {David A. Nicholson and Gregory C. Rutledge},\n" + "title = {Molecular simulation of flow-enhanced nucleation in n-eicosane melts under steady shear and uniaxial extension},\n" + "journal = {The Journal of Chemical Physics},\n" + "volume = {145},\n" + "number = {24},\n" + "pages = {244903},\n" + "year = {2016}\n" + "}\n\n"; + /* ---------------------------------------------------------------------- * Parse the remaing keywords, do some error checking, and initalize * temp/pressure fixes @@ -102,6 +116,7 @@ char ** FixNHUef::arg_kludge(int &narg, char **arg, int &rem) FixNHUef::FixNHUef(LAMMPS *lmp, int narg, char **arg) : FixNH(lmp, narg, arg_kludge(narg,arg,rem)) { + if (lmp->citeme) lmp->citeme->add(cite_user_uef_package); //initialization erate[0] = erate[1] = 0; From 2a06b75af84cb9c41e4eefb7bfd32dc2a6492160 Mon Sep 17 00:00:00 2001 From: David Nicholson Date: Fri, 29 Sep 2017 15:36:41 -0400 Subject: [PATCH 07/21] doc revisions --- doc/src/compute_pressure_uef.txt | 2 +- doc/src/compute_temp_uef.txt | 2 +- doc/src/fix_nh_uef.txt | 6 +++--- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt index e2e49da26d..065fc04441 100644 --- a/doc/src/compute_pressure_uef.txt +++ b/doc/src/compute_pressure_uef.txt @@ -13,7 +13,7 @@ compute pressure/uef command :h3 compute ID group-ID pressure/uef temp-ID keyword ... :pre ID, group-ID are documented in "compute"_compute.html command -pressure = style name of this compute command +pressure/uef = style name of this compute command temp-ID = ID of compute that calculates temperature, can be NULL if not needed zero or more keywords may be appended keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt index 562ad89b66..acd3a6218d 100644 --- a/doc/src/compute_temp_uef.txt +++ b/doc/src/compute_temp_uef.txt @@ -13,7 +13,7 @@ compute temp/uef command :h3 compute ID group-ID temp/uef :pre ID, group-ID are documented in "compute"_compute.html command -temp = style name of this compute command :ul +temp/uef = style name of this compute command :ul [Examples:] diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt index 250d5624d0..9cee428d83 100644 --- a/doc/src/fix_nh_uef.txt +++ b/doc/src/fix_nh_uef.txt @@ -11,7 +11,7 @@ fix npt/uef command :h3 [Syntax:] -fix ID group-ID style_name erate eps_x eps_y temp Tstart Tstop Tdamp keyword value ... :pre +fix ID group-ID style_name erate edot_x edot_y temp Tstart Tstop Tdamp keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l style_name = {nvt/uef} or {npt/uef} :l @@ -31,7 +31,7 @@ keyword = {ext} or {strain} or {iso} or {x} or {y} or {z} or {tchain} or {pchain fix uniax_nvt all nvt/uef temp 400 400 100 erate 0.00001 -0.000005 fix biax_nvt all nvt/uef temp 400 400 100 erate 0.000005 0.000005 fix uniax_npt all npt/uef temp 400 400 300 iso 1 1 3000 erate 0.00001 -0.000005 ext yz -fix biax_npt all npt/uef temp 400 400 100 erate 0.00001 -0.000005 :pre +fix biax_npt all npt/uef temp 400 400 100 erate -0.00001 0.000005 x 1 1 3000 :pre [Description:] @@ -92,7 +92,7 @@ in "fix npt"_fix_nh.html. There are two ways to control the pressure using this fix. The first method involves using the {ext} keyword along with the {iso} pressure style. With this method, the pressure is controlled by scaling the simulation box isotropically to achieve the average pressure only in the directions specified by {ext}. -For example, if the {ext} values is set to {xy}, the average pressure (Pxx+Pyy)/2 +For example, if the {ext} value is set to {xy}, the average pressure (Pxx+Pyy)/2 will be controlled. This example command will control the total hydrostatic pressure under uniaxial tension: From 4ef63feea7d328eb7b34d1126381a221201f42e1 Mon Sep 17 00:00:00 2001 From: David Nicholson Date: Fri, 29 Sep 2017 15:50:31 -0400 Subject: [PATCH 08/21] reran examples --- ...al.g++.1 => log.22Sep17.npt_biaxial.g++.1} | 34 ++- .../npt_biaxial/log.22Sep17.npt_biaxial.g++.4 | 284 ++++++++++++++++++ .../npt_biaxial/log.30Jul16.npt_biaxial.g++.4 | 276 ----------------- .../log.22Sep17.npt_uniaxial.g++.1 | 2 + .../log.22Sep17.npt_uniaxial.g++.4 | 281 +++++++++++++++++ .../log.30Jul16.npt_uniaxial.g++.1 | 273 ----------------- .../log.30Jul16.npt_uniaxial.g++.4 | 273 ----------------- 7 files changed, 588 insertions(+), 835 deletions(-) rename examples/USER/uef/npt_biaxial/{log.30Jul16.npt_biaxial.g++.1 => log.22Sep17.npt_biaxial.g++.1} (92%) create mode 100644 examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 delete mode 100644 examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.4 create mode 100644 examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.1 create mode 100644 examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.4 delete mode 100644 examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.1 delete mode 100644 examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.4 diff --git a/examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.1 b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1 similarity index 92% rename from examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.1 rename to examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1 index 65f0184d13..12de8ff8be 100644 --- a/examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.1 +++ b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (30 Jul 2016) +LAMMPS (22 Sep 2017) # biaxial NPT deformation of WCA fluid units lj @@ -38,14 +38,19 @@ thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] thermo 50 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.62256 ghost atom cutoff = 1.62256 - binsize = 0.811281 -> bins = 11 11 11 -Memory usage per processor = 2.40217 Mbytes -Step 1_press[ 1_press[ 1_press[ + binsize = 0.811281, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.742 | 2.742 | 2.742 Mbytes +Step c_1_press[1] c_1_press[2] c_1_press[3] 0 6.3937851 7.0436438 6.4461087 50 7.9020345 7.303289 14.733929 100 8.3214325 8.385843 13.166247 @@ -247,20 +252,20 @@ Step 1_press[ 1_press[ 1_press[ 9900 5.0133498 4.7456254 9.4572653 9950 5.3318846 4.6643122 10.096292 10000 5.2227687 4.8924305 9.5894615 -Loop time of 4.42114 on 1 procs for 10000 steps with 500 atoms +Loop time of 4.5628 on 1 procs for 10000 steps with 500 atoms -Performance: 977122.661 tau/day, 2261.858 timesteps/s +Performance: 946786.828 tau/day, 2191.636 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.72321 | 0.72321 | 0.72321 | 0.0 | 16.36 -Neigh | 2.6161 | 2.6161 | 2.6161 | 0.0 | 59.17 -Comm | 0.30217 | 0.30217 | 0.30217 | 0.0 | 6.83 -Output | 0.0034378 | 0.0034378 | 0.0034378 | 0.0 | 0.08 -Modify | 0.67004 | 0.67004 | 0.67004 | 0.0 | 15.16 -Other | | 0.1062 | | | 2.40 +Pair | 0.70711 | 0.70711 | 0.70711 | 0.0 | 15.50 +Neigh | 2.7689 | 2.7689 | 2.7689 | 0.0 | 60.69 +Comm | 0.30715 | 0.30715 | 0.30715 | 0.0 | 6.73 +Output | 0.0036616 | 0.0036616 | 0.0036616 | 0.0 | 0.08 +Modify | 0.67113 | 0.67113 | 0.67113 | 0.0 | 14.71 +Other | | 0.1048 | | | 2.30 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -273,4 +278,7 @@ Total # of neighbors = 3340 Ave neighs/atom = 6.68 Neighbor list builds = 4580 Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + Total wall time: 0:00:04 diff --git a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 new file mode 100644 index 0000000000..7a2c553fcf --- /dev/null +++ b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 @@ -0,0 +1,284 @@ +LAMMPS (22 Sep 2017) +# biaxial NPT deformation of WCA fluid + +units lj +atom_style atomic + + +pair_style lj/cut 1.122562 +read_data data.wca + orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities +pair_coeff 1 1 1.0 1.0 +pair_modify shift yes + +neighbor 0.5 bin +neigh_modify delay 0 + +change_box all triclinic + triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) + +# these commads show the different methods that may be used to impose +# a constant stress through isotropic or anisotropic coupling +fix 1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z +#fix 1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5 erate 0.5 0.5 ext xyz + +fix 2 all momentum 100 linear 1 1 1 + +#dump 1 all atom 25 dump.lammpstrj + +#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs + +thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] + +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.62256 + ghost atom cutoff = 1.62256 + binsize = 0.811281, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.71 | 2.71 | 2.71 Mbytes +Step c_1_press[1] c_1_press[2] c_1_press[3] + 0 6.3937851 7.0436438 6.4461087 + 50 7.9020345 7.303289 14.733929 + 100 8.3214325 8.385843 13.166247 + 150 5.7168419 5.6083988 9.7224198 + 200 3.8875348 4.0840705 7.9912973 + 250 4.2933724 4.2410519 7.7200953 + 300 4.5452314 4.2434949 8.6709832 + 350 5.446489 5.6166962 11.300536 + 400 6.0682558 5.7787878 12.106852 + 450 5.3884296 5.5066688 9.9100012 + 500 4.8046418 4.7115986 9.9769201 + 550 4.9043933 4.6240966 9.319336 + 600 4.6843238 4.9571246 9.5325487 + 650 5.1952989 5.195648 9.6187047 + 700 5.4163364 5.2938289 10.136655 + 750 5.6723178 5.0670261 11.415221 + 800 5.9379901 5.6402916 10.815209 + 850 5.0695389 5.3021432 10.742859 + 900 4.6498961 4.7111912 9.8453525 + 950 4.4811637 5.1701321 9.4217645 + 1000 4.750149 4.2420768 9.3510788 + 1050 4.5973376 5.2046787 9.8633025 + 1100 4.7879516 4.9051338 9.8658577 + 1150 5.0528775 5.5048673 10.110905 + 1200 4.992684 5.2482046 9.9610521 + 1250 4.8475843 4.8499105 9.575365 + 1300 5.2930179 5.0593567 10.869332 + 1350 5.4722311 5.0830422 10.69342 + 1400 4.8165864 4.9851485 10.042141 + 1450 4.6276548 4.5643142 9.2306057 + 1500 5.0197119 4.5470582 8.7204541 + 1550 4.878215 5.158312 10.264148 + 1600 5.4917782 5.3121766 10.273923 + 1650 5.4381825 5.1698438 9.9823968 + 1700 4.9206398 5.2852701 9.5806048 + 1750 4.9226742 4.7164231 8.932911 + 1800 4.9733613 4.8776709 9.6638069 + 1850 5.1327098 4.8503755 10.170281 + 1900 5.9114024 6.0045781 10.515973 + 1950 5.2332897 5.7899133 10.436353 + 2000 5.286098 5.3874673 10.124669 + 2050 5.0167541 5.490974 9.6476751 + 2100 5.3933017 5.372036 9.7187857 + 2150 4.8288683 4.7937794 9.2252452 + 2200 5.0760371 4.8515447 9.8373704 + 2250 5.5626387 5.5509581 10.274505 + 2300 5.1009883 4.9400598 10.300516 + 2350 5.3148808 5.4689154 9.9240269 + 2400 4.8720251 4.9341152 10.32893 + 2450 5.1964062 5.394913 9.6729737 + 2500 4.9715986 5.1500527 10.925999 + 2550 5.1240848 4.3358732 9.9783677 + 2600 4.7387276 4.3732544 9.4545219 + 2650 4.6787161 4.7001729 9.4697272 + 2700 5.5549736 5.4437977 10.581898 + 2750 5.523176 5.0416156 10.338311 + 2800 5.3864512 5.439205 10.079435 + 2850 5.5675261 5.2310133 10.524415 + 2900 5.2628013 5.3641439 10.160587 + 2950 4.7300407 4.6838026 8.9617691 + 3000 5.1744361 4.5005726 10.487918 + 3050 5.2239211 5.3030573 10.376913 + 3100 5.1016236 5.0700451 9.4697833 + 3150 5.0661402 5.142376 9.5591223 + 3200 5.397775 4.9229072 10.389504 + 3250 5.5515257 5.2365437 10.265586 + 3300 5.844715 5.2552463 10.065811 + 3350 4.888658 5.0636003 10.129015 + 3400 4.55264 5.0703435 8.7178922 + 3450 4.992088 5.2487278 10.087295 + 3500 5.3469913 4.785277 9.8944509 + 3550 5.217282 5.3011196 9.6306807 + 3600 5.8928519 4.9717327 10.897022 + 3650 6.0118006 5.9046823 11.2352 + 3700 5.0667885 5.2572827 10.266895 + 3750 4.8133435 4.8991016 9.4760522 + 3800 4.5125756 4.8295067 9.0226716 + 3850 4.4651224 4.678168 8.7474636 + 3900 4.9811965 4.687682 9.0547397 + 3950 5.2387906 5.4772104 10.416997 + 4000 5.3576384 5.896421 10.524538 + 4050 5.8265842 5.7449599 10.527804 + 4100 5.2276111 5.1866643 10.1139 + 4150 5.2739201 4.8869905 9.5700647 + 4200 4.7943987 4.4305245 8.8436208 + 4250 4.9285996 4.9591754 10.121985 + 4300 5.5289613 6.0688348 10.898698 + 4350 5.6673111 5.3636174 10.569902 + 4400 4.7882862 5.3060196 10.050009 + 4450 5.1309456 4.9776646 9.8804906 + 4500 5.0629205 4.7277565 8.7584435 + 4550 5.1009496 4.8110658 9.4666416 + 4600 5.5858872 5.4123191 12.263621 + 4650 5.5585654 5.8537188 10.258869 + 4700 4.8064416 5.060519 10.153314 + 4750 4.7181218 5.0631685 9.3624778 + 4800 4.871496 4.8872111 9.7435175 + 4850 4.8297469 4.6464864 9.6852358 + 4900 5.5682142 5.5530971 10.073983 + 4950 5.1322491 5.3402989 10.283117 + 5000 5.4516954 5.6198027 11.223665 + 5050 5.1488128 5.1092478 10.375804 + 5100 4.4000207 4.7355267 9.5152048 + 5150 4.6501804 5.0426405 9.5383808 + 5200 4.8589325 4.9719089 8.8114996 + 5250 5.0343815 4.8677968 10.967149 + 5300 5.6710156 5.5661349 11.436985 + 5350 5.2243912 5.101865 9.9427717 + 5400 4.3337053 4.6325695 9.6917273 + 5450 4.6217314 5.0129144 9.1988349 + 5500 5.1014594 4.7848497 10.516995 + 5550 5.0465061 4.9173385 9.3561229 + 5600 4.8643636 4.860697 10.428496 + 5650 5.6536439 5.4434563 10.014098 + 5700 4.9734376 4.7193345 9.5610177 + 5750 5.3414745 5.148175 11.048378 + 5800 5.4363776 5.0286279 10.85538 + 5850 5.1060233 5.1350774 9.3190058 + 5900 4.5611096 4.4980661 8.8914749 + 5950 4.4264357 4.7757911 8.4601102 + 6000 5.059237 5.6791366 10.779186 + 6050 5.3216769 5.8043231 10.290497 + 6100 5.0261845 5.3700963 10.430661 + 6150 5.8132491 5.5245642 10.675176 + 6200 5.2346131 5.21174 10.332249 + 6250 5.3756188 4.787094 9.7496811 + 6300 5.2054751 4.7341501 10.034542 + 6350 5.1908834 4.9041004 9.2702025 + 6400 4.2876866 4.3860725 9.3793733 + 6450 5.1264657 4.8049065 9.9620589 + 6500 5.019625 5.4901247 9.821544 + 6550 5.3251841 5.3680612 10.021716 + 6600 5.2494437 4.8680991 9.5942134 + 6650 5.1676116 5.6642827 9.8496995 + 6700 5.423067 5.4226985 10.171776 + 6750 4.9274053 5.3926204 9.8502911 + 6800 4.9887802 5.0472917 10.111779 + 6850 4.7201661 4.83946 9.6275293 + 6900 4.6270723 4.3137963 9.9911883 + 6950 4.7942567 4.8427671 9.6135269 + 7000 5.0437851 5.1894655 9.8059441 + 7050 5.4225853 5.6730348 10.380611 + 7100 5.3526725 5.366095 10.809916 + 7150 5.4601926 5.288364 10.565143 + 7200 5.1693092 5.2974578 9.849408 + 7250 4.636056 4.9049993 8.886325 + 7300 4.3959701 4.329844 9.2339636 + 7350 4.565932 4.5362817 9.4502211 + 7400 4.8815031 5.2467956 9.533884 + 7450 5.0423354 5.4958195 10.746164 + 7500 5.4986547 5.4120911 10.642538 + 7550 4.8194458 4.6515196 9.3519793 + 7600 4.3485953 4.9262925 9.2856337 + 7650 4.6044397 4.8926749 9.1169078 + 7700 4.887369 5.14193 10.058145 + 7750 5.5487873 5.5141636 11.432779 + 7800 5.4104699 5.5487467 11.192853 + 7850 4.854184 5.057851 9.6193733 + 7900 4.6510371 4.6445148 9.5905654 + 7950 4.9814759 4.7704719 9.4965789 + 8000 4.7758292 5.1937876 9.4849264 + 8050 4.7782452 4.5663494 9.7289633 + 8100 4.8225098 5.3648384 9.5979339 + 8150 6.0148826 5.3649476 11.154587 + 8200 5.827507 5.5169147 10.572628 + 8250 5.0297257 5.1234338 9.3020411 + 8300 4.6046603 4.5570973 8.8827391 + 8350 5.3644712 5.1981202 10.229824 + 8400 5.1883813 5.4376828 9.9731365 + 8450 5.3046097 5.7491798 11.164114 + 8500 5.2650074 5.1202378 10.749497 + 8550 4.7905964 5.2786974 10.550609 + 8600 4.617429 4.7393959 9.0461214 + 8650 4.6256633 4.5693007 9.3443004 + 8700 4.7009411 4.030803 8.9360375 + 8750 5.3789708 4.760461 9.8339628 + 8800 5.7463414 5.4243514 10.470581 + 8850 5.157278 5.5842305 11.486137 + 8900 5.0475937 5.1205189 10.086114 + 8950 4.5184928 4.7852537 9.5368998 + 9000 4.5055459 4.9449201 9.4658539 + 9050 5.0035206 4.9128749 9.0698534 + 9100 4.821598 4.8336838 9.3036301 + 9150 5.4258294 5.6834484 10.695099 + 9200 6.3446945 5.3907995 11.225169 + 9250 4.8853033 5.4945962 9.8970725 + 9300 4.6751599 4.9974483 9.754605 + 9350 4.8758504 4.905638 9.4632169 + 9400 4.7936798 4.9838949 10.272661 + 9450 5.0815525 5.4520368 9.6176533 + 9500 5.6312632 5.5596893 10.352406 + 9550 5.0373182 5.0675577 10.549761 + 9600 4.9424044 4.7441107 9.6055995 + 9650 4.4176445 4.6896883 8.9482316 + 9700 4.8480419 4.9664903 10.140515 + 9750 5.0869492 5.6569476 10.616019 + 9800 5.6557237 5.4549563 10.34766 + 9850 5.4099086 5.6741059 10.187811 + 9900 4.8200517 4.931253 9.0858362 + 9950 4.6887887 4.9860091 10.703951 + 10000 5.266225 5.2694816 9.5314566 +Loop time of 2.5963 on 4 procs for 10000 steps with 500 atoms + +Performance: 1663904.185 tau/day, 3851.630 timesteps/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.28841 | 0.29049 | 0.29324 | 0.3 | 11.19 +Neigh | 1.0622 | 1.078 | 1.0899 | 1.0 | 41.52 +Comm | 0.55877 | 0.56907 | 0.58702 | 1.4 | 21.92 +Output | 0.0028131 | 0.0034448 | 0.0052423 | 1.8 | 0.13 +Modify | 0.54339 | 0.54747 | 0.54917 | 0.3 | 21.09 +Other | | 0.1078 | | | 4.15 + +Nlocal: 125 ave 128 max 121 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Nghost: 453.75 ave 460 max 450 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 845 ave 874 max 787 min +Histogram: 1 0 0 0 0 0 0 1 1 1 + +Total # of neighbors = 3380 +Ave neighs/atom = 6.76 +Neighbor list builds = 4592 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:02 diff --git a/examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.4 b/examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.4 deleted file mode 100644 index 4ff3551605..0000000000 --- a/examples/USER/uef/npt_biaxial/log.30Jul16.npt_biaxial.g++.4 +++ /dev/null @@ -1,276 +0,0 @@ -LAMMPS (30 Jul 2016) -# biaxial NPT deformation of WCA fluid - -units lj -atom_style atomic - - -pair_style lj/cut 1.122562 -read_data data.wca - orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 500 atoms - reading velocities ... - 500 velocities -pair_coeff 1 1 1.0 1.0 -pair_modify shift yes - -neighbor 0.5 bin -neigh_modify delay 0 - -change_box all triclinic - triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) - -# these commads show the different methods that may be used to impose -# a constant stress through isotropic or anisotropic coupling -fix 1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z -#fix 1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5 erate 0.5 0.5 ext xyz - -fix 2 all momentum 100 linear 1 1 1 - -#dump 1 all atom 25 dump.lammpstrj - -#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs - -thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] - -thermo 50 -run 10000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.62256 - ghost atom cutoff = 1.62256 - binsize = 0.811281 -> bins = 11 11 11 -Memory usage per processor = 2.38201 Mbytes -Step 1_press[ 1_press[ 1_press[ - 0 6.3937851 7.0436438 6.4461087 - 50 7.9020345 7.303289 14.733929 - 100 8.3214325 8.385843 13.166247 - 150 5.7168419 5.6083988 9.7224198 - 200 3.8875348 4.0840705 7.9912973 - 250 4.2933724 4.2410519 7.7200953 - 300 4.5452314 4.2434949 8.6709832 - 350 5.446489 5.6166962 11.300536 - 400 6.0682558 5.7787878 12.106852 - 450 5.3884296 5.5066688 9.9100012 - 500 4.8046418 4.7115986 9.9769201 - 550 4.9043933 4.6240966 9.319336 - 600 4.6843238 4.9571246 9.5325487 - 650 5.1952989 5.195648 9.6187047 - 700 5.4163364 5.2938289 10.136655 - 750 5.6723178 5.0670261 11.415221 - 800 5.9379901 5.6402916 10.815209 - 850 5.0695389 5.3021432 10.742859 - 900 4.6498961 4.7111912 9.8453525 - 950 4.4811637 5.170132 9.4217644 - 1000 4.7501491 4.2420769 9.3510789 - 1050 4.5973375 5.2046786 9.8633021 - 1100 4.7879517 4.905134 9.8658575 - 1150 5.0528775 5.5048673 10.110907 - 1200 4.9926837 5.2482072 9.961051 - 1250 4.8475661 4.8499052 9.5753719 - 1300 5.2929874 5.0593404 10.869345 - 1350 5.4722108 5.083063 10.693408 - 1400 4.816304 4.9851244 10.041255 - 1450 4.6280905 4.5646059 9.2298768 - 1500 5.01985 4.5471327 8.721625 - 1550 4.8741077 5.1549887 10.256565 - 1600 5.4916921 5.3197646 10.281538 - 1650 5.4772243 5.1837045 9.9982297 - 1700 4.9419503 5.2869766 9.5825456 - 1750 5.0000465 4.6358961 8.8873809 - 1800 5.0008968 4.9755404 10.274347 - 1850 5.3911106 5.0602442 10.252838 - 1900 5.6306791 5.5982927 11.287727 - 1950 5.0117663 4.9037147 9.9079668 - 2000 4.9080829 4.8206128 9.2645313 - 2050 4.7794302 4.5942332 9.22621 - 2100 5.1197536 4.884078 9.9557557 - 2150 5.5674448 4.9602998 10.825168 - 2200 5.9993278 5.484917 11.201052 - 2250 5.619781 5.2475017 10.382149 - 2300 4.7213112 4.5460993 10.254176 - 2350 4.4310098 4.6363048 8.2696199 - 2400 4.2798177 4.1485611 8.2037599 - 2450 5.0414399 5.2572888 10.126969 - 2500 5.2807077 5.4633007 10.424033 - 2550 5.4538601 5.3268172 10.06153 - 2600 4.9750473 5.2268468 10.433373 - 2650 4.8397032 5.2258654 9.8686538 - 2700 4.8943282 4.7637421 9.8715146 - 2750 4.8870682 4.7334316 9.2096451 - 2800 4.7611053 4.9820018 9.0797655 - 2850 4.826047 5.2478652 10.549013 - 2900 5.5999506 5.0160442 9.6169413 - 2950 5.6210454 5.1519961 10.23173 - 3000 5.2132243 5.1449194 9.9778889 - 3050 5.651798 5.5919186 10.772823 - 3100 4.8453492 4.6559497 9.175617 - 3150 4.359467 4.9901271 8.512659 - 3200 4.5724772 4.8788065 9.2580198 - 3250 5.3195893 5.6518901 10.562311 - 3300 5.4571458 5.9778537 11.804991 - 3350 5.1322763 5.280149 10.894715 - 3400 4.9393514 4.9051844 9.3048468 - 3450 4.6741698 4.6317669 9.4965959 - 3500 4.8634066 4.9618835 8.926419 - 3550 4.7096981 4.4196734 9.5607265 - 3600 5.1871839 5.3427606 9.9467134 - 3650 5.7619975 5.2486309 10.359674 - 3700 5.2563068 5.4591612 10.360825 - 3750 5.2492743 5.4861677 9.7648858 - 3800 5.0335744 5.2240642 9.6668438 - 3850 5.1003253 5.0865548 11.111281 - 3900 5.2978019 5.2126205 10.581896 - 3950 5.0067291 5.2645911 10.750446 - 4000 4.6513682 4.7407991 9.3959165 - 4050 4.1903728 4.4021987 8.8451881 - 4100 5.0089655 4.4961608 9.7363416 - 4150 5.1557684 5.6110293 10.804015 - 4200 5.2607824 5.3663361 10.663617 - 4250 5.0134036 5.1164765 9.3320261 - 4300 4.2919496 4.6118896 9.2176556 - 4350 4.9118467 4.9766595 9.8989104 - 4400 5.7694762 5.2410849 10.660891 - 4450 5.3793656 5.4714178 10.784611 - 4500 5.187077 5.0952514 9.6404449 - 4550 4.9522826 4.5959954 10.30975 - 4600 4.9512246 5.0305627 10.295169 - 4650 5.8017637 5.3485687 10.411051 - 4700 5.2499784 4.8217382 10.077816 - 4750 4.9961796 4.9148313 9.4660475 - 4800 4.8958835 4.6546838 9.1730325 - 4850 4.7408482 5.1862514 9.9399226 - 4900 4.999383 4.9513486 9.5506941 - 4950 5.0375134 4.63474 10.325618 - 5000 5.0274884 5.391675 9.592851 - 5050 5.3817822 5.5141892 11.43286 - 5100 5.533224 5.1489534 10.56325 - 5150 4.4884587 4.8979144 9.7439562 - 5200 4.7352575 4.2854079 8.8328248 - 5250 4.6347427 4.7579757 9.5316726 - 5300 4.9765192 5.1378784 9.7376039 - 5350 5.1899675 4.9469798 10.699202 - 5400 5.0178189 5.47536 9.707559 - 5450 4.9537295 5.1651951 9.7430567 - 5500 4.8448459 4.6800231 9.297621 - 5550 5.1703386 4.865903 10.090954 - 5600 5.6293349 5.4332687 10.047955 - 5650 5.2729245 6.180173 10.259202 - 5700 5.1034054 5.2082315 10.031079 - 5750 5.0982009 5.0158875 10.3517 - 5800 4.8139573 4.8454398 10.001093 - 5850 5.3237843 4.9860148 10.493724 - 5900 4.421652 4.7147453 10.30137 - 5950 5.3475173 4.8489279 9.7495241 - 6000 5.013939 4.796874 9.7433063 - 6050 5.1111778 5.2773346 10.245638 - 6100 5.1484609 5.2230939 9.9800589 - 6150 5.0101213 5.0702323 9.7021038 - 6200 4.5881964 5.2635287 9.3903355 - 6250 5.5340791 5.5956851 10.809705 - 6300 5.3121762 5.3679934 9.4683653 - 6350 5.072589 5.0111289 10.494452 - 6400 5.3134876 5.3779245 11.439347 - 6450 4.9930408 5.3215491 10.287925 - 6500 4.6925854 4.4527123 9.3141266 - 6550 4.5127115 4.5276223 9.2970101 - 6600 4.6857945 5.0039986 9.8782575 - 6650 5.4210348 4.6775837 10.404812 - 6700 5.416291 5.1705872 10.935776 - 6750 5.2396825 5.0306589 10.14922 - 6800 5.3579349 4.9442072 10.510841 - 6850 4.8287972 4.4930847 9.4697502 - 6900 4.9688784 4.5977364 10.004321 - 6950 4.7853293 4.5578984 9.0727469 - 7000 5.0589506 4.9662362 11.04237 - 7050 5.2657677 5.3989373 10.712811 - 7100 5.5373555 5.6700228 10.099215 - 7150 4.7085526 4.4207863 9.417028 - 7200 4.7480934 4.8575585 9.970864 - 7250 5.2732588 5.211703 9.8573725 - 7300 5.0152654 5.5514349 11.104278 - 7350 4.9255785 5.3533123 10.69476 - 7400 5.1041241 5.0597338 9.5918592 - 7450 4.7333067 4.584844 10.820426 - 7500 4.9157751 5.0274623 10.706391 - 7550 4.8231717 5.2251684 9.7721097 - 7600 4.5115685 4.6809903 9.1230191 - 7650 4.76928 5.0869557 9.2881957 - 7700 5.1014383 5.4733369 9.9024386 - 7750 5.7812792 5.6404429 10.895814 - 7800 5.451651 5.4137204 10.471661 - 7850 4.7982757 5.2043999 10.046712 - 7900 4.4490306 4.546108 8.3934233 - 7950 4.3147055 4.489834 8.8833017 - 8000 5.0558378 5.1022203 11.21385 - 8050 6.0715673 5.9289687 12.007167 - 8100 5.4463621 5.8686057 9.7475724 - 8150 4.6295786 4.5658519 8.9353979 - 8200 4.4109788 4.4122705 8.8574801 - 8250 4.9903375 5.2807872 10.024069 - 8300 5.2930602 5.7480682 10.33242 - 8350 5.6166755 5.3279586 10.761278 - 8400 5.2344331 5.3991078 10.261601 - 8450 4.9395736 4.8421048 10.544976 - 8500 4.8692729 4.4538669 10.38133 - 8550 4.7746965 4.5959252 10.413873 - 8600 4.4344376 4.9176179 9.0368016 - 8650 5.0230802 4.7795825 8.5121429 - 8700 4.9279145 4.8844196 10.145405 - 8750 5.343116 5.7462499 11.191805 - 8800 5.4073851 5.1952022 9.6534892 - 8850 5.6085471 5.1332845 10.28282 - 8900 4.9077946 5.1446696 9.236557 - 8950 4.9416647 5.2071136 10.106251 - 9000 5.4201564 5.3733264 11.081109 - 9050 5.9648951 5.5501112 12.621681 - 9100 4.8947991 5.2187898 10.470022 - 9150 4.48197 4.1036268 8.4201904 - 9200 4.3946543 4.3973715 8.5340163 - 9250 5.3021965 5.2717867 9.2560849 - 9300 5.1768568 5.8272523 10.232503 - 9350 5.7291082 5.7641611 11.622836 - 9400 5.5971415 6.0957826 11.948662 - 9450 4.6317008 4.8550521 9.7699372 - 9500 4.3364192 4.4197985 8.8085022 - 9550 4.4961662 4.5930997 9.6064493 - 9600 4.901858 5.3789866 10.044551 - 9650 5.2916208 4.9071387 9.9083075 - 9700 4.8995154 4.78658 9.3871144 - 9750 5.5045136 5.3070515 10.969147 - 9800 5.2729372 6.0714054 11.027892 - 9850 4.8794625 5.2788176 10.100819 - 9900 4.6173961 4.6918339 9.2090718 - 9950 4.7478539 4.6911854 8.6831286 - 10000 4.9331146 5.3771408 11.489778 -Loop time of 2.62782 on 4 procs for 10000 steps with 500 atoms - -Performance: 1643945.149 tau/day, 3805.429 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.29968 | 0.30667 | 0.31341 | 1.2 | 11.67 -Neigh | 1.0173 | 1.0395 | 1.0668 | 2.1 | 39.56 -Comm | 0.55804 | 0.59161 | 0.62132 | 3.5 | 22.51 -Output | 0.0028653 | 0.0035743 | 0.0056112 | 2.0 | 0.14 -Modify | 0.5692 | 0.5732 | 0.57625 | 0.4 | 21.81 -Other | | 0.1132 | | | 4.31 - -Nlocal: 125 ave 130 max 121 min -Histogram: 1 1 0 0 0 0 1 0 0 1 -Nghost: 452.25 ave 455 max 449 min -Histogram: 1 0 0 0 0 1 1 0 0 1 -Neighs: 837 ave 882 max 804 min -Histogram: 2 0 0 0 0 0 1 0 0 1 - -Total # of neighbors = 3348 -Ave neighs/atom = 6.696 -Neighbor list builds = 4598 -Dangerous builds = 0 -Total wall time: 0:00:02 diff --git a/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.1 b/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.1 new file mode 100644 index 0000000000..726ef62179 --- /dev/null +++ b/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.1 @@ -0,0 +1,2 @@ +LAMMPS (22 Sep 2017) +Total wall time: 0:00:02 diff --git a/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.4 b/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.4 new file mode 100644 index 0000000000..fd366b7711 --- /dev/null +++ b/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.4 @@ -0,0 +1,281 @@ +LAMMPS (22 Sep 2017) +# uniaxial NVT deformation of WCA fluid + +units lj +atom_style atomic + + +pair_style lj/cut 1.122562 +read_data data.wca + orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities +pair_coeff 1 1 1.0 1.0 +pair_modify shift yes + +neighbor 0.5 bin +neigh_modify delay 0 + +change_box all triclinic + triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) + +fix 1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5 + +fix 2 all momentum 100 linear 1 1 1 + +#dump 1 all atom 25 dump.lammpstrj + +#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs + +thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] + +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.62256 + ghost atom cutoff = 1.62256 + binsize = 0.811281, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.71 | 2.71 | 2.71 Mbytes +Step c_1_press[1] c_1_press[2] c_1_press[3] + 0 6.3937851 7.0436438 6.4461087 + 50 10.369902 10.999889 6.5437384 + 100 12.411384 13.145871 7.8892802 + 150 12.88182 12.114068 7.5155182 + 200 10.375571 10.979773 6.5624056 + 250 10.158901 10.251273 5.4525068 + 300 10.011314 9.8371382 5.4031393 + 350 9.4890008 9.7992108 5.054963 + 400 9.1715116 9.2647886 4.9600208 + 450 9.8495961 9.3353483 4.986786 + 500 9.5903809 8.576173 4.8252116 + 550 8.8057509 9.7152078 4.9089022 + 600 8.9743682 10.031277 4.8924072 + 650 10.233852 9.3059527 5.1977058 + 700 9.2361906 9.6439971 5.0923762 + 750 10.449751 9.5911465 5.2548714 + 800 9.8366858 9.9873885 4.9456956 + 850 10.266351 9.9620134 5.0602713 + 900 9.6325811 9.3910947 5.1466627 + 950 9.1911905 9.1518996 4.8275336 + 1000 9.2871726 9.8508563 5.2674079 + 1050 9.7052021 10.291782 5.1603606 + 1100 9.9425831 10.361849 5.5520586 + 1150 10.37757 10.265897 5.5997238 + 1200 9.636703 10.354446 5.4138755 + 1250 9.2075215 9.1705175 4.9806575 + 1300 9.7125393 8.7247632 4.8527793 + 1350 10.146277 9.8323819 4.8958397 + 1400 9.1957181 9.7052513 5.2335098 + 1450 9.4667213 8.9007965 4.7073369 + 1500 9.0965389 9.8398957 4.8891559 + 1550 10.06178 9.8138538 5.1638382 + 1600 10.143509 9.7138732 5.0784492 + 1650 9.9512338 9.8872687 5.1954485 + 1700 9.3001767 8.4717446 4.9066425 + 1750 9.1538623 9.449051 4.9792008 + 1800 10.647126 9.9223864 4.9100709 + 1850 10.58929 9.5949045 5.4586105 + 1900 9.1522315 10.1302 5.1997482 + 1950 9.101169 9.4253005 5.1420221 + 2000 9.6193051 9.6907925 5.1624939 + 2050 9.6709026 9.9097494 5.0839389 + 2100 10.057719 9.4467483 4.8687849 + 2150 9.1739276 9.1641054 5.1634915 + 2200 9.5136146 9.2946745 4.9764961 + 2250 9.3797544 9.1230688 5.0899386 + 2300 10.298029 9.4044845 5.2381589 + 2350 9.9207185 9.7553339 5.1366828 + 2400 9.6642531 9.8963683 4.8646464 + 2450 8.7643842 9.3435464 4.9072249 + 2500 9.5049695 9.5989949 5.0092494 + 2550 9.6320496 9.4008794 4.8200251 + 2600 9.903178 9.4782306 5.0650137 + 2650 9.4189501 9.2165039 5.1789521 + 2700 9.0208832 9.348362 4.8609921 + 2750 9.6783103 9.8040877 5.0079603 + 2800 10.031195 10.619877 5.374209 + 2850 9.8303748 10.254827 5.3671813 + 2900 9.1249173 8.5172277 5.2143577 + 2950 9.0730525 9.2540699 4.8573951 + 3000 9.9958033 9.6279178 5.1505831 + 3050 9.3665306 9.5285363 5.1160245 + 3100 9.299668 9.0685264 5.0511145 + 3150 9.0579805 9.4816527 5.2936574 + 3200 9.5941 9.7325027 5.1824229 + 3250 10.194794 9.4171587 5.443428 + 3300 9.5927373 9.4430409 4.8998086 + 3350 9.9600944 9.4542266 5.5225391 + 3400 9.7209098 10.024835 5.535451 + 3450 8.6519155 8.9415312 4.8385083 + 3500 10.096352 8.8783306 4.9350231 + 3550 9.3491636 9.5548236 5.2751 + 3600 9.6919611 9.7076185 5.1635464 + 3650 10.481089 9.4863551 5.3286659 + 3700 9.5756116 9.2201941 5.226026 + 3750 9.6434932 9.5295221 5.0288715 + 3800 9.9269327 10.205704 4.7808382 + 3850 9.3189899 10.218335 4.83239 + 3900 9.609462 9.3080222 5.0195027 + 3950 9.5231033 8.869665 5.1015894 + 4000 9.6412436 9.3303396 4.8401661 + 4050 9.8174742 9.4591309 5.4392126 + 4100 9.7799256 9.6304628 4.672532 + 4150 9.8013021 10.139168 5.5527338 + 4200 9.2342593 9.2257279 5.2050637 + 4250 10.018762 10.415623 5.389449 + 4300 9.0369099 8.3453432 4.8345057 + 4350 9.6482435 9.2127862 4.7007287 + 4400 9.1131695 8.4018843 5.1782917 + 4450 9.1035579 9.6671216 4.8282646 + 4500 8.9284156 9.8070543 4.8713415 + 4550 10.131312 9.8932255 4.9533532 + 4600 10.077058 10.137857 5.0295905 + 4650 10.173958 9.1894558 5.6784615 + 4700 9.4202409 8.6802878 5.0213632 + 4750 9.9258459 9.3402009 5.3392346 + 4800 9.8529686 9.5514806 5.1122451 + 4850 10.161646 9.244328 5.1681917 + 4900 9.3419622 9.8193483 5.2391261 + 4950 9.4263728 10.150522 5.043291 + 5000 9.3869223 9.1981116 5.1708012 + 5050 8.9996015 9.4572528 5.1843173 + 5100 8.9894979 9.5093357 4.8005208 + 5150 9.7942953 9.7335166 5.198425 + 5200 9.8904105 9.8505698 5.3255803 + 5250 10.222488 9.0105229 5.0736676 + 5300 9.1670895 10.615218 5.323205 + 5350 9.7642772 9.6199466 5.5903157 + 5400 8.8178616 9.1035263 4.9848621 + 5450 9.6779115 9.5531466 5.0626435 + 5500 9.4723384 9.8744061 4.8594102 + 5550 9.2659141 9.3866112 5.1213249 + 5600 9.9307711 10.011157 4.7073137 + 5650 9.1360772 10.050505 5.3293825 + 5700 8.9098929 9.7579153 5.3489592 + 5750 8.7670629 9.3719349 5.4463723 + 5800 9.0459529 8.7757212 4.8544378 + 5850 9.434501 9.7207864 4.7607373 + 5900 9.1211752 9.7909617 5.4247162 + 5950 10.12889 10.010702 5.360621 + 6000 9.703862 9.3482478 5.0059776 + 6050 9.9038104 8.8812394 5.1991618 + 6100 9.5438555 9.4415027 4.9217198 + 6150 10.192211 9.2429673 5.1715813 + 6200 10.306686 9.1384768 4.7312526 + 6250 9.4873042 9.9164005 5.0562414 + 6300 9.8842909 9.730243 5.1300241 + 6350 9.9418731 9.9679301 5.0582982 + 6400 9.4128222 9.292455 5.4644225 + 6450 8.7305012 8.0605057 4.5415131 + 6500 8.8577233 8.5832574 4.40194 + 6550 9.6163915 9.2509075 5.1138801 + 6600 10.128781 10.078794 5.4904826 + 6650 9.6019333 9.5285605 5.58386 + 6700 10.021737 10.073117 5.1420822 + 6750 10.495681 10.002678 5.0176241 + 6800 9.9675843 10.053135 5.3183498 + 6850 9.2289727 9.2937883 5.2061573 + 6900 9.3004627 9.8324369 4.9496725 + 6950 9.02096 9.3364941 4.9229962 + 7000 9.5391177 9.1122871 5.1137302 + 7050 9.5599 9.5978836 5.1530405 + 7100 9.4939385 9.641504 5.3032985 + 7150 9.7088291 9.7821494 5.0252857 + 7200 9.6044672 8.9831056 4.7110805 + 7250 9.1933876 9.044105 5.1760484 + 7300 8.8666209 8.8262052 5.0675085 + 7350 8.9601722 8.8080504 4.6713412 + 7400 9.7343434 9.230838 5.0227894 + 7450 10.465298 10.086546 5.3538547 + 7500 9.8348497 9.6682345 5.6155581 + 7550 9.2055261 9.9530385 5.2999975 + 7600 10.058087 10.359037 5.5097355 + 7650 10.049127 9.1073265 5.677653 + 7700 9.8658364 9.3018637 5.1476764 + 7750 9.1199366 9.0783067 5.0848865 + 7800 8.8578293 8.7974398 5.2016434 + 7850 9.775635 9.463061 5.3655492 + 7900 9.295538 9.5095055 4.8011116 + 7950 9.6493214 9.8679316 5.5265297 + 8000 9.8347059 9.766271 5.0480481 + 8050 10.221272 9.8343303 5.1569604 + 8100 9.9470574 9.6982535 5.2138091 + 8150 9.7416712 9.9761168 5.3335775 + 8200 9.6885832 9.7871945 5.084485 + 8250 9.4437905 9.6080847 5.1152245 + 8300 9.8251187 9.381407 5.2040497 + 8350 9.997553 10.13024 5.4380783 + 8400 8.964249 9.7006666 5.3283399 + 8450 9.0154607 8.9476167 4.9831421 + 8500 9.7376641 8.943646 4.8864283 + 8550 9.0838444 9.2479888 4.9685049 + 8600 9.6403296 9.8366009 5.0968951 + 8650 9.6635046 10.308254 5.2703839 + 8700 10.365594 10.611924 5.1621352 + 8750 9.805264 10.361514 5.1519855 + 8800 9.5028336 10.227006 5.2248281 + 8850 10.183228 9.921676 5.3720572 + 8900 9.3635214 9.6744843 5.2400037 + 8950 10.670314 9.9503151 5.1614572 + 9000 9.7127361 9.6573131 5.3563693 + 9050 8.7056986 9.0613731 5.046923 + 9100 8.9478272 9.0640872 4.9287586 + 9150 8.8313013 8.5112475 5.2262306 + 9200 9.364301 8.959883 5.0174211 + 9250 10.288615 9.1790518 5.0426516 + 9300 9.617956 9.7241075 5.3777373 + 9350 10.0358 9.5309547 5.4949469 + 9400 9.8158206 10.060424 5.3424158 + 9450 10.005718 9.1139373 4.9685999 + 9500 9.806939 9.6244612 5.1818962 + 9550 10.28972 9.3960873 5.0642479 + 9600 10.312876 9.4252906 5.2704439 + 9650 9.6829433 9.9125054 4.9184741 + 9700 9.6234227 10.008167 5.1544723 + 9750 10.025877 9.4306579 5.3817937 + 9800 9.3702702 9.6149983 4.8804752 + 9850 9.4719715 9.1649874 5.1584215 + 9900 8.9906714 9.1807845 4.8599792 + 9950 9.1661525 9.1219335 4.8148579 + 10000 9.1946626 9.3436899 5.0765307 +Loop time of 2.3144 on 4 procs for 10000 steps with 500 atoms + +Performance: 1866574.813 tau/day, 4320.775 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.24989 | 0.25356 | 0.25618 | 0.5 | 10.96 +Neigh | 1.0785 | 1.0971 | 1.1047 | 1.0 | 47.40 +Comm | 0.56674 | 0.57565 | 0.59467 | 1.5 | 24.87 +Output | 0.0038562 | 0.0045416 | 0.006454 | 1.6 | 0.20 +Modify | 0.26644 | 0.2701 | 0.27307 | 0.5 | 11.67 +Other | | 0.1134 | | | 4.90 + +Nlocal: 125 ave 135 max 121 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 462.75 ave 468 max 457 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Neighs: 861.75 ave 946 max 830 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 3447 +Ave neighs/atom = 6.894 +Neighbor list builds = 4556 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:02 diff --git a/examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.1 b/examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.1 deleted file mode 100644 index 1d6530ff46..0000000000 --- a/examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.1 +++ /dev/null @@ -1,273 +0,0 @@ -LAMMPS (30 Jul 2016) -# uniaxial NVT deformation of WCA fluid - -units lj -atom_style atomic - - -pair_style lj/cut 1.122562 -read_data data.wca - orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 500 atoms - reading velocities ... - 500 velocities -pair_coeff 1 1 1.0 1.0 -pair_modify shift yes - -neighbor 0.5 bin -neigh_modify delay 0 - -change_box all triclinic - triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) - -fix 1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5 - -fix 2 all momentum 100 linear 1 1 1 - -#dump 1 all atom 25 dump.lammpstrj - -#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs - -thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] - -thermo 50 -run 10000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.62256 - ghost atom cutoff = 1.62256 - binsize = 0.811281 -> bins = 11 11 11 -Memory usage per processor = 2.40217 Mbytes -Step 1_press[ 1_press[ 1_press[ - 0 6.3937851 7.0436438 6.4461087 - 50 10.369902 10.999889 6.5437384 - 100 12.411384 13.145871 7.8892802 - 150 12.88182 12.114068 7.5155182 - 200 10.375571 10.979773 6.5624056 - 250 10.158901 10.251273 5.4525068 - 300 10.011314 9.8371382 5.4031393 - 350 9.4890008 9.7992108 5.054963 - 400 9.1715116 9.2647886 4.9600208 - 450 9.8495961 9.3353483 4.986786 - 500 9.5903809 8.576173 4.8252116 - 550 8.8057509 9.7152078 4.9089022 - 600 8.9743682 10.031277 4.8924072 - 650 10.233852 9.3059527 5.1977058 - 700 9.2361906 9.6439971 5.0923763 - 750 10.449751 9.5911465 5.2548714 - 800 9.8366857 9.9873885 4.9456956 - 850 10.266351 9.9620134 5.0602713 - 900 9.6325813 9.3910946 5.1466624 - 950 9.1911919 9.1519006 4.8275345 - 1000 9.2871712 9.8508501 5.2674099 - 1050 9.7052035 10.291793 5.160359 - 1100 9.9425552 10.361827 5.5520484 - 1150 10.377563 10.26588 5.5997436 - 1200 9.6368269 10.354413 5.4137873 - 1250 9.2071055 9.1706334 4.9800411 - 1300 9.7140516 8.7257777 4.8536943 - 1350 10.145983 9.8247797 4.8921813 - 1400 9.1998975 9.6935675 5.2269871 - 1450 9.4838136 8.9035726 4.6867121 - 1500 9.066389 9.811658 4.8875316 - 1550 10.007083 9.8946118 5.204609 - 1600 9.722137 9.9291588 5.326712 - 1650 9.7424614 9.6995966 5.3577819 - 1700 9.7185135 9.5922931 5.385856 - 1750 9.6368481 8.1414594 5.0046079 - 1800 9.8065782 9.6798036 4.92473 - 1850 9.0463737 10.024205 5.6495695 - 1900 9.0774484 10.527582 5.0363426 - 1950 9.1691461 10.049703 4.8517514 - 2000 9.7619602 10.049532 5.2088038 - 2050 9.9203348 9.8056395 5.7699852 - 2100 9.1455665 9.5864018 5.1410542 - 2150 8.8501135 9.7917307 5.141824 - 2200 9.1433685 9.8168548 5.1742441 - 2250 9.3248968 10.454532 5.5456356 - 2300 10.210505 9.361499 5.0935226 - 2350 9.5041186 9.598986 5.2451005 - 2400 8.968896 9.2811921 4.7799868 - 2450 9.8201159 10.133892 4.9981817 - 2500 9.4421084 9.7875766 5.4124809 - 2550 9.6410643 9.9148309 5.0603288 - 2600 9.3810676 9.5346849 5.3233836 - 2650 9.2340337 8.7233538 5.0361302 - 2700 9.405597 9.7848488 4.7537042 - 2750 9.9447412 9.2366502 4.9736459 - 2800 10.189443 9.452684 5.624362 - 2850 9.6680124 9.0941543 5.0101469 - 2900 8.4350889 9.1595018 4.7706866 - 2950 9.0056117 9.3498593 4.7655963 - 3000 9.4795416 9.7400747 5.4705868 - 3050 9.6605264 9.4558374 5.1240166 - 3100 9.681451 9.7966554 5.3174458 - 3150 9.7887528 9.7371194 4.9349103 - 3200 9.9720054 9.5592538 5.2306417 - 3250 10.185023 9.9436037 5.4127312 - 3300 9.9670676 9.6069307 5.026261 - 3350 9.0090411 9.5975249 4.8881019 - 3400 9.6535707 9.748683 4.9933873 - 3450 9.7774977 9.7570511 4.8512619 - 3500 9.7250053 10.36386 5.4057249 - 3550 9.567788 9.773413 5.3936671 - 3600 9.2094148 9.0211247 5.2328675 - 3650 9.3512098 9.73407 4.576624 - 3700 9.159074 9.2611591 5.2996448 - 3750 9.4772798 8.9792211 5.1007079 - 3800 9.3898357 9.1150609 5.2126508 - 3850 9.2466312 9.1460651 4.867472 - 3900 9.9316993 9.3061137 5.1219265 - 3950 9.2550913 9.780254 5.371885 - 4000 10.005356 9.7328972 5.2535791 - 4050 9.5228242 9.5134113 5.4181393 - 4100 9.576808 10.082425 5.1272491 - 4150 10.20265 9.6667058 5.529118 - 4200 9.9443671 10.09427 5.6163734 - 4250 9.4956875 9.9462818 5.0820085 - 4300 10.350144 10.003702 5.1621505 - 4350 10.119486 9.8691507 5.4913457 - 4400 9.4991604 10.516185 5.2512264 - 4450 9.0812854 9.2835603 5.1695714 - 4500 9.7538478 8.5298834 4.5954607 - 4550 9.8920394 9.3581299 5.202587 - 4600 9.2694921 9.3338291 5.201958 - 4650 10.925818 9.5062049 4.8694531 - 4700 11.020014 10.130224 5.582409 - 4750 9.5005142 9.3571561 5.456739 - 4800 9.6670147 9.6628702 5.0451252 - 4850 9.134147 9.1308788 4.7950594 - 4900 9.7466206 8.6171443 4.8716275 - 4950 9.0397505 9.1996036 5.2010502 - 5000 9.6898652 9.8914655 5.3959279 - 5050 10.06771 9.7523891 5.3690408 - 5100 10.000963 9.6279379 5.4077384 - 5150 9.8686159 10.179702 5.0686824 - 5200 9.8866247 9.725152 5.4350049 - 5250 9.2068346 10.214424 5.3187713 - 5300 9.713992 9.8069045 5.496359 - 5350 9.423852 9.364085 5.2144606 - 5400 9.4350241 9.5584633 5.0339001 - 5450 10.555124 10.784922 5.1938072 - 5500 9.4147344 10.33187 5.4360602 - 5550 9.8514653 9.6575827 5.4959779 - 5600 9.3138107 9.6592624 4.941387 - 5650 9.1224809 8.7112257 5.0435936 - 5700 8.8289158 10.749686 4.8916132 - 5750 9.7200279 10.030606 5.2033161 - 5800 9.8439873 9.6289015 5.5131934 - 5850 9.6257294 9.4128988 4.9196038 - 5900 9.7490214 9.5776313 5.0301815 - 5950 9.1430855 10.108944 5.1406243 - 6000 9.3358644 9.5633737 4.9787073 - 6050 9.4432774 8.9464304 5.1466052 - 6100 8.8878373 9.5048946 4.9190238 - 6150 9.6451898 9.2419823 5.0159841 - 6200 9.5042173 8.9414307 5.2634247 - 6250 9.0896505 9.7230651 5.3340322 - 6300 8.8100599 8.8781352 5.4117914 - 6350 9.3104601 9.0233294 5.3136432 - 6400 9.368101 9.6387362 4.7833216 - 6450 10.334343 9.8384149 5.3606204 - 6500 9.8824036 10.022627 6.0857086 - 6550 9.7034443 10.026765 5.17604 - 6600 9.3757845 9.899268 5.2301359 - 6650 10.540821 10.4343 5.5287065 - 6700 9.6317649 9.8923579 5.6045768 - 6750 9.5982772 10.07897 5.1221451 - 6800 10.239883 10.189967 5.3167447 - 6850 10.017271 9.7680902 5.229621 - 6900 9.6200416 10.129301 5.1998759 - 6950 9.0361417 8.923798 5.1652612 - 7000 9.3153521 9.063054 4.6860773 - 7050 8.6434091 9.0363436 4.7811975 - 7100 9.4955395 9.3830541 5.022538 - 7150 9.3392402 9.1847119 5.1544622 - 7200 9.4676321 9.8370036 4.8854442 - 7250 9.5115882 10.350324 4.9780525 - 7300 9.6025583 9.6247917 5.473794 - 7350 9.8919524 10.049446 4.9816931 - 7400 9.6814319 9.9410894 5.265078 - 7450 9.4130955 10.191436 5.2531256 - 7500 9.8114668 8.8461635 5.0562894 - 7550 10.321567 9.4730124 5.2043655 - 7600 9.5059024 9.8330367 5.0749721 - 7650 10.067084 10.606423 5.5598818 - 7700 10.896159 10.084281 5.5159718 - 7750 9.754306 10.162301 5.2475876 - 7800 9.7278145 9.801009 5.0685504 - 7850 9.8639905 10.323104 5.2458864 - 7900 9.7246799 9.1377357 5.1841319 - 7950 10.381792 9.6977533 5.0977386 - 8000 9.7265224 9.2999829 4.7925571 - 8050 9.5203288 9.3144956 4.7539211 - 8100 9.6900973 9.6614063 5.304712 - 8150 9.713677 9.9154149 4.8178575 - 8200 9.4733597 9.8948632 5.036112 - 8250 9.7783036 9.9554334 5.3355682 - 8300 9.4034783 9.9156801 5.5539279 - 8350 9.2984025 9.2013949 5.0753991 - 8400 9.9299078 9.6166801 5.115776 - 8450 9.526737 9.3312125 4.7800587 - 8500 9.581956 10.065906 4.9756092 - 8550 9.2767953 9.326006 5.3024978 - 8600 9.799968 8.4660845 5.0199109 - 8650 9.8985354 10.127852 4.9098064 - 8700 8.7952691 10.521133 5.6840528 - 8750 9.8299997 9.5588553 5.3085734 - 8800 9.0811776 9.5704532 5.1684993 - 8850 9.8303571 9.7618932 5.1251259 - 8900 9.9238794 9.9654863 5.2999683 - 8950 10.851304 9.9682289 5.4133763 - 9000 9.5523794 9.1890766 5.1469144 - 9050 9.7461948 8.9611236 4.9490826 - 9100 10.138917 9.6757567 5.0473544 - 9150 9.4869835 9.4786575 5.0142464 - 9200 10.263518 10.079135 5.1493398 - 9250 9.8691684 9.0908275 5.3221203 - 9300 9.8586707 9.4177643 5.1525265 - 9350 9.3375816 9.9167208 5.4846207 - 9400 9.5603903 9.4813199 4.6237495 - 9450 10.30892 9.5217736 5.6163214 - 9500 9.327949 9.9831649 4.8923915 - 9550 9.8421656 9.3202702 5.3352046 - 9600 8.8543704 9.4556702 4.6430041 - 9650 10.103399 9.2161072 4.8658062 - 9700 9.507811 9.9647378 5.227369 - 9750 9.4988096 8.9942893 5.2491418 - 9800 9.8007958 9.234452 5.1740203 - 9850 9.6029685 10.076042 5.023107 - 9900 9.4035691 10.13782 5.2775777 - 9950 9.6517135 10.355994 5.3035779 - 10000 9.9157616 9.7741952 5.5269431 -Loop time of 4.303 on 1 procs for 10000 steps with 500 atoms - -Performance: 1003950.961 tau/day, 2323.961 timesteps/s -99.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.69667 | 0.69667 | 0.69667 | 0.0 | 16.19 -Neigh | 2.699 | 2.699 | 2.699 | 0.0 | 62.72 -Comm | 0.30701 | 0.30701 | 0.30701 | 0.0 | 7.13 -Output | 0.003968 | 0.003968 | 0.003968 | 0.0 | 0.09 -Modify | 0.49374 | 0.49374 | 0.49374 | 0.0 | 11.47 -Other | | 0.1026 | | | 2.38 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 908 ave 908 max 908 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3489 ave 3489 max 3489 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3489 -Ave neighs/atom = 6.978 -Neighbor list builds = 4567 -Dangerous builds = 0 -Total wall time: 0:00:04 diff --git a/examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.4 b/examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.4 deleted file mode 100644 index f977bf4e7d..0000000000 --- a/examples/USER/uef/nvt_uniaxial/log.30Jul16.npt_uniaxial.g++.4 +++ /dev/null @@ -1,273 +0,0 @@ -LAMMPS (30 Jul 2016) -# uniaxial NVT deformation of WCA fluid - -units lj -atom_style atomic - - -pair_style lj/cut 1.122562 -read_data data.wca - orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 500 atoms - reading velocities ... - 500 velocities -pair_coeff 1 1 1.0 1.0 -pair_modify shift yes - -neighbor 0.5 bin -neigh_modify delay 0 - -change_box all triclinic - triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) - -fix 1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5 - -fix 2 all momentum 100 linear 1 1 1 - -#dump 1 all atom 25 dump.lammpstrj - -#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs - -thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] - -thermo 50 -run 10000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.62256 - ghost atom cutoff = 1.62256 - binsize = 0.811281 -> bins = 11 11 11 -Memory usage per processor = 2.38201 Mbytes -Step 1_press[ 1_press[ 1_press[ - 0 6.3937851 7.0436438 6.4461087 - 50 10.369902 10.999889 6.5437384 - 100 12.411384 13.145871 7.8892802 - 150 12.88182 12.114068 7.5155182 - 200 10.375571 10.979773 6.5624056 - 250 10.158901 10.251273 5.4525068 - 300 10.011314 9.8371382 5.4031393 - 350 9.4890008 9.7992108 5.054963 - 400 9.1715116 9.2647886 4.9600208 - 450 9.8495961 9.3353483 4.986786 - 500 9.5903809 8.576173 4.8252116 - 550 8.8057509 9.7152078 4.9089022 - 600 8.9743682 10.031277 4.8924072 - 650 10.233852 9.3059527 5.1977058 - 700 9.2361906 9.6439971 5.0923762 - 750 10.449751 9.5911465 5.2548714 - 800 9.8366858 9.9873885 4.9456956 - 850 10.266351 9.9620134 5.0602713 - 900 9.6325811 9.3910947 5.1466627 - 950 9.1911905 9.1518997 4.8275335 - 1000 9.2871725 9.8508561 5.2674079 - 1050 9.7052018 10.291782 5.1603606 - 1100 9.942582 10.361849 5.5520591 - 1150 10.37757 10.265893 5.5997259 - 1200 9.6367107 10.354442 5.4138733 - 1250 9.2075329 9.1705 4.9806587 - 1300 9.7125232 8.724748 4.852827 - 1350 10.146185 9.8320894 4.8958299 - 1400 9.1958247 9.7053023 5.2334931 - 1450 9.4656613 8.9011194 4.7069541 - 1500 9.0964228 9.8379154 4.8889701 - 1550 10.074953 9.8121208 5.1614034 - 1600 10.14322 9.7113028 5.0901612 - 1650 9.9377801 9.8831912 5.2226793 - 1700 9.4144883 8.5248477 4.9447402 - 1750 9.0729219 9.612432 5.1999941 - 1800 10.067363 9.8211216 5.1464764 - 1850 9.3044429 8.9752352 5.0515339 - 1900 9.4123739 9.1810527 5.3356061 - 1950 9.3009721 10.013851 4.9527398 - 2000 9.7741829 10.11286 5.3818321 - 2050 9.6991106 9.7815812 5.1979016 - 2100 9.2977435 9.4310005 5.0893893 - 2150 10.325992 10.388415 4.9253076 - 2200 10.193251 10.389764 5.4164579 - 2250 9.9386988 9.63934 5.1685251 - 2300 9.3128664 10.496199 5.423297 - 2350 8.692096 9.761347 5.1356802 - 2400 9.4532892 9.2946894 5.3127538 - 2450 9.026436 8.8042728 4.9305279 - 2500 8.9458518 9.6338731 5.1530972 - 2550 8.9457961 9.7730997 5.1588 - 2600 9.4313048 9.0489105 4.9937356 - 2650 9.1625701 10.03039 4.9384831 - 2700 10.135274 9.9106295 5.1582637 - 2750 9.7419819 9.7329998 5.4813308 - 2800 9.6793568 10.137218 4.9126985 - 2850 9.8286116 9.8283148 5.2372177 - 2900 9.2766894 9.5302835 5.1206658 - 2950 9.6537203 9.8713609 5.2640351 - 3000 9.704446 10.360629 5.2470236 - 3050 9.289114 10.210593 4.9955164 - 3100 9.5854695 9.0377602 5.0387963 - 3150 9.4489179 9.0145734 4.9089788 - 3200 8.9221328 8.8805863 4.7910012 - 3250 8.9268792 8.6855592 4.7798689 - 3300 9.5280088 9.6859376 5.1021255 - 3350 9.7469167 9.7039449 5.3654161 - 3400 10.163823 10.247303 5.3206912 - 3450 10.328168 9.2596091 5.3903402 - 3500 10.280033 10.087996 5.3980267 - 3550 9.5278822 10.057563 4.9949376 - 3600 9.3705739 9.9639827 5.1315405 - 3650 10.003355 9.0323131 5.288539 - 3700 9.5814093 9.742063 4.9937322 - 3750 9.1121545 9.9600773 5.2621763 - 3800 8.4753486 9.2930472 4.8939508 - 3850 9.309286 9.0227214 4.9323125 - 3900 9.0283302 10.048011 5.0801404 - 3950 10.193343 10.279252 5.4390015 - 4000 9.5170246 9.8575174 5.3284718 - 4050 9.0306235 9.4210217 4.7042159 - 4100 9.7801264 10.267131 4.8946632 - 4150 10.161985 10.327002 5.3719225 - 4200 10.242291 9.5148633 5.2938589 - 4250 9.67955 10.025696 5.517063 - 4300 9.0818798 9.655456 5.0976568 - 4350 9.3181275 8.8534154 4.9252792 - 4400 9.4111133 8.9481402 4.8338338 - 4450 10.219905 10.0317 5.3278766 - 4500 9.9718967 9.9808168 5.2294123 - 4550 9.7194794 9.7613441 5.3369724 - 4600 9.4826038 9.5426517 5.1951956 - 4650 9.5794203 8.4729044 4.9375856 - 4700 9.6409231 10.059765 4.9659309 - 4750 9.0853564 9.6062246 5.1560466 - 4800 9.5805015 10.26319 5.1395845 - 4850 8.8662041 9.4757304 5.1729905 - 4900 9.6230855 10.239009 5.1382048 - 4950 10.401327 9.5494971 5.2688637 - 5000 10.433047 9.9017863 5.4626886 - 5050 10.318188 9.2998964 5.4707543 - 5100 9.6958274 9.206341 5.0269859 - 5150 9.5477552 10.099142 5.3760873 - 5200 9.4904189 9.4403777 5.1638292 - 5250 9.8421539 8.7828543 4.8612713 - 5300 9.7354196 9.357113 4.9059656 - 5350 9.9183987 9.4337973 5.2986167 - 5400 10.045743 9.8399757 5.0930923 - 5450 9.6414177 10.169944 5.3868716 - 5500 10.035214 9.5316451 4.912222 - 5550 9.16334 9.3853532 5.2319683 - 5600 9.5075535 9.2548959 5.4425531 - 5650 9.3854437 9.0700172 4.9845383 - 5700 9.1868937 9.3061525 4.9155762 - 5750 9.4785528 9.8271693 4.9974045 - 5800 9.7809419 10.070618 5.3699816 - 5850 10.791132 10.572676 5.3816834 - 5900 10.091884 10.036391 5.7604455 - 5950 9.4492785 8.9938163 4.9812227 - 6000 9.2296463 10.334517 5.6374553 - 6050 9.9339781 9.1097471 4.6847041 - 6100 10.369857 9.261491 5.3354256 - 6150 9.9444024 9.5330721 5.2413981 - 6200 9.1507255 9.2108005 4.7010871 - 6250 9.6093995 9.2275894 4.8659261 - 6300 9.0300283 9.149341 4.9305141 - 6350 9.6718904 9.5721387 4.9560051 - 6400 9.615362 10.030978 4.8786582 - 6450 10.343763 10.184481 5.2027613 - 6500 9.3452563 9.7249417 5.2318842 - 6550 9.9489414 10.373436 4.9258407 - 6600 10.083741 10.87974 5.3665699 - 6650 9.431476 9.7944015 5.4214407 - 6700 9.3430129 10.032417 4.8538936 - 6750 10.253341 9.5667637 5.3838115 - 6800 8.9695591 9.888476 4.7973343 - 6850 9.6952765 9.3339082 4.8432603 - 6900 9.1038139 9.6295207 4.8572214 - 6950 9.5374663 9.0498856 5.2316356 - 7000 8.6844415 9.1416318 4.9513449 - 7050 9.6271147 8.8341922 5.135948 - 7100 9.3889214 9.6771129 5.1106028 - 7150 9.4697432 9.9959141 4.8762717 - 7200 9.9545962 9.5556848 5.2760968 - 7250 10.153728 10.396722 5.4066282 - 7300 9.5633599 9.8262997 5.5238788 - 7350 10.476059 9.8526241 4.9928222 - 7400 9.5848947 9.389115 5.1177333 - 7450 9.3917853 9.8395056 5.5201002 - 7500 9.2406374 9.4598141 4.9336365 - 7550 9.1325284 9.0585 5.007436 - 7600 9.5045307 9.5164648 4.8310378 - 7650 9.5165952 9.5154581 5.3199138 - 7700 9.1167042 9.3283907 4.9548988 - 7750 9.5408306 10.191558 5.1889476 - 7800 9.2362359 9.5066276 5.4139251 - 7850 9.9533215 9.3418618 5.0073354 - 7900 9.063471 9.2389687 5.1529568 - 7950 9.6887619 9.3363144 5.0264365 - 8000 10.244559 10.352116 5.3898068 - 8050 10.522656 9.7844249 5.648648 - 8100 10.456047 10.108097 5.234203 - 8150 9.0497599 10.3333 5.5526068 - 8200 9.1341912 9.7046196 4.7491692 - 8250 9.3297032 9.2513325 4.9471519 - 8300 9.9385635 9.8432553 4.9102209 - 8350 9.506086 9.3628428 5.4489526 - 8400 9.7575572 9.6628477 4.7835143 - 8450 9.4234184 9.6901535 5.2506704 - 8500 9.1019018 9.4713605 4.9996292 - 8550 8.9668254 9.2297952 4.9015639 - 8600 10.000082 9.852912 5.1235791 - 8650 9.6677771 9.8825377 5.0888713 - 8700 9.5220305 9.6140025 5.2621374 - 8750 9.769165 9.1639605 4.942283 - 8800 10.214712 9.0544214 5.0977658 - 8850 10.050644 8.9450446 4.876467 - 8900 9.7066878 9.8028705 5.1098917 - 8950 9.8322209 9.5247394 5.1258681 - 9000 10.116755 9.9220422 5.2801505 - 9050 9.671068 9.448618 5.1789641 - 9100 8.6872235 9.8346401 4.8940421 - 9150 9.8181714 9.652061 4.9136383 - 9200 9.5400873 9.9027439 5.3147415 - 9250 9.2344784 9.9272383 5.397571 - 9300 9.0207063 9.2498921 5.0643988 - 9350 10.648665 9.0509298 5.0354353 - 9400 9.7266263 9.5319347 5.4323366 - 9450 9.5044169 9.7968623 5.2079039 - 9500 9.0459316 9.6916313 5.1584987 - 9550 9.1265901 10.045493 4.9476229 - 9600 9.896449 9.509792 5.5305989 - 9650 9.2957435 9.4288068 5.1885785 - 9700 9.6000499 8.7187335 5.0900953 - 9750 9.5997652 9.4810899 4.8707106 - 9800 9.2198937 9.7067006 5.4461186 - 9850 9.8794169 10.051937 5.0361319 - 9900 9.9783069 9.9785092 5.2066807 - 9950 9.0880268 9.5659803 5.3678011 - 10000 9.6972182 9.9076171 5.1538951 -Loop time of 2.23728 on 4 procs for 10000 steps with 500 atoms - -Performance: 1930919.704 tau/day, 4469.722 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.26111 | 0.26444 | 0.26854 | 0.5 | 11.82 -Neigh | 1.0268 | 1.037 | 1.0467 | 0.7 | 46.35 -Comm | 0.5321 | 0.55022 | 0.56515 | 1.6 | 24.59 -Output | 0.003746 | 0.0045477 | 0.006809 | 1.9 | 0.20 -Modify | 0.26509 | 0.26827 | 0.27182 | 0.5 | 11.99 -Other | | 0.1128 | | | 5.04 - -Nlocal: 125 ave 128 max 123 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Nghost: 468.25 ave 470 max 467 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Neighs: 869.75 ave 895 max 843 min -Histogram: 1 0 0 0 1 0 1 0 0 1 - -Total # of neighbors = 3479 -Ave neighs/atom = 6.958 -Neighbor list builds = 4555 -Dangerous builds = 0 -Total wall time: 0:00:02 From 4524b0fa83fad6bf14a2aa6e5e27a19ac547ab66 Mon Sep 17 00:00:00 2001 From: David Nicholson Date: Fri, 29 Sep 2017 16:54:46 -0400 Subject: [PATCH 09/21] rename arg_kludge to uef_arg_kludge --- src/USER-UEF/fix_nh_uef.cpp | 4 ++-- src/USER-UEF/fix_nh_uef.h | 3 ++- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp index 1bc9386ad6..fe342f1efd 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -44,7 +44,7 @@ enum{ISO,ANISO,TRICLINIC}; so FixNH::FixNH() only sees the keywords it knows. Save the numer of remaining keywords in rem. ---------------------------------------------------------------------- */ -char ** FixNHUef::arg_kludge(int &narg, char **arg, int &rem) +char ** LAMMPS_NS::uef_arg_kludge(int &narg, char **arg, int &rem) { int iarg = 3; bool flags[3]= {false,false,false}; @@ -114,7 +114,7 @@ static const char cite_user_uef_package[] = * temp/pressure fixes ---------------------------------------------------------------------- */ FixNHUef::FixNHUef(LAMMPS *lmp, int narg, char **arg) : - FixNH(lmp, narg, arg_kludge(narg,arg,rem)) + FixNH(lmp, narg, uef_arg_kludge(narg,arg,rem)) { if (lmp->citeme) lmp->citeme->add(cite_user_uef_package); diff --git a/src/USER-UEF/fix_nh_uef.h b/src/USER-UEF/fix_nh_uef.h index 46916005a3..8b0f07a34b 100644 --- a/src/USER-UEF/fix_nh_uef.h +++ b/src/USER-UEF/fix_nh_uef.h @@ -21,6 +21,8 @@ #include "fix_nh.h" namespace LAMMPS_NS { + +char **uef_arg_kludge(int&, char**, int&); class FixNHUef : public FixNH { public: FixNHUef(class LAMMPS *, int, char **); @@ -46,7 +48,6 @@ class FixNHUef : public FixNH { virtual int size_restart_global(); virtual void nve_x(); virtual void nve_v(); - char **arg_kludge(int&, char**, int&); void rotate_x(double [3][3]); void inv_rotate_x(double[3][3]); void rotate_v(double[3][3]); From 0c7879e9024309c54b5c5caf39c4b242b8e9e7b5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 2 Oct 2017 15:53:28 -0400 Subject: [PATCH 10/21] provide compatibility entries in FixNH option parsing for new USER-UEF package --- src/fix_nh.cpp | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index c99c7a34bd..f95bde95d0 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -353,6 +353,15 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : } else if (strcmp(arg[iarg],"disc") == 0) { iarg++; + // keywords erate, strain, and ext are also parsed in fix/nh/uef + + } else if (strcmp(arg[iarg],"erate") == 0) { + iarg += 3; + } else if (strcmp(arg[iarg],"strain") == 0) { + iarg += 3; + } else if (strcmp(arg[iarg],"ext") == 0) { + iarg += 2; + } else error->all(FLERR,"Illegal fix nvt/npt/nph command"); } From 81be9b37de9c9379ec96dabf5d31f9e931b5f7b7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 2 Oct 2017 17:15:13 -0400 Subject: [PATCH 11/21] formatting, whitespace and include file/constants cleanup --- src/USER-UEF/compute_pressure_uef.cpp | 12 ++++++------ src/USER-UEF/compute_pressure_uef.h | 10 +++++----- src/USER-UEF/compute_temp_uef.cpp | 8 ++++---- src/USER-UEF/compute_temp_uef.h | 8 ++++---- src/USER-UEF/dump_cfg_uef.cpp | 6 +++--- src/USER-UEF/dump_cfg_uef.h | 2 +- src/USER-UEF/fix_nh_uef.cpp | 6 +++--- src/USER-UEF/fix_npt_uef.cpp | 5 ----- src/USER-UEF/fix_npt_uef.h | 2 +- src/USER-UEF/fix_nvt_uef.cpp | 5 ----- src/USER-UEF/fix_nvt_uef.h | 2 +- src/USER-UEF/uef_utils.cpp | 24 +++++++++++++----------- src/USER-UEF/uef_utils.h | 20 +++++--------------- 13 files changed, 46 insertions(+), 64 deletions(-) diff --git a/src/USER-UEF/compute_pressure_uef.cpp b/src/USER-UEF/compute_pressure_uef.cpp index e9bbdf0cf4..5c6ef0940f 100644 --- a/src/USER-UEF/compute_pressure_uef.cpp +++ b/src/USER-UEF/compute_pressure_uef.cpp @@ -13,9 +13,9 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include "mpi.h" -#include "string.h" -#include "stdlib.h" +#include +#include +#include #include "compute_pressure_uef.h" #include "fix_nh_uef.h" #include "update.h" @@ -118,7 +118,7 @@ void ComputePressureUef::compute_vector() if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for " - "tensor components with kspace_style msm"); + "tensor components with kspace_style msm"); // invoke temperature if it hasn't been already @@ -131,7 +131,7 @@ void ComputePressureUef::compute_vector() if (dimension == 3) { inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd); - virial_compute(6,3); + virial_compute(6,3); if (in_fix) virial_rot(virial,rot); else @@ -182,7 +182,7 @@ void ComputePressureUef::virial_rot(double *x, const double r[3][3]) // [00 10 20 ] [ 0 3 4 ] [00 01 02 ] // [01 11 21 ] [ 3 1 5 ] [10 11 12 ] // [02 12 22 ] [ 4 5 2 ] [20 21 22 ] - for (int k = 0; k<3; ++k) + for (int k = 0; k<3; ++k) { t[0][k] = x[0]*r[0][k] + x[3]*r[1][k] + x[4]*r[2][k]; t[1][k] = x[3]*r[0][k] + x[1]*r[1][k] + x[5]*r[2][k]; diff --git a/src/USER-UEF/compute_pressure_uef.h b/src/USER-UEF/compute_pressure_uef.h index 2f591b64d8..d3a4d3195c 100644 --- a/src/USER-UEF/compute_pressure_uef.h +++ b/src/USER-UEF/compute_pressure_uef.h @@ -1,4 +1,4 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov @@ -31,11 +31,11 @@ class ComputePressureUef : public ComputePressure { ComputePressureUef(class LAMMPS *, int, char **); virtual ~ComputePressureUef(){} virtual void init(); - virtual void compute_vector(); - virtual double compute_scalar(); + virtual void compute_vector(); + virtual double compute_scalar(); void update_rot(); bool in_fix; //true if this compute is used in fix/nvt/npt - + protected: bool ext_flags[3]; // true if used in average output pressure @@ -57,7 +57,7 @@ only additions are: E: Can't use compute pressure/uef without defining a fix nvt/npt/uef -Self-explanatory. +Self-explanatory. W: The temperature used in compute pressure/uef is not of style temp/uef diff --git a/src/USER-UEF/compute_temp_uef.cpp b/src/USER-UEF/compute_temp_uef.cpp index 8c8c9be293..2947adc879 100644 --- a/src/USER-UEF/compute_temp_uef.cpp +++ b/src/USER-UEF/compute_temp_uef.cpp @@ -13,8 +13,8 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include "string.h" -#include "stdlib.h" +#include +#include #include "compute_temp_uef.h" #include "fix_nh_uef.h" #include "update.h" @@ -28,7 +28,7 @@ using namespace LAMMPS_NS; * Base constructor initialized to use rotation matrix * ----------------------------------------------------------------------*/ ComputeTempUef::ComputeTempUef(LAMMPS *lmp, int narg, char **arg) : - ComputeTemp(lmp, narg, arg) + ComputeTemp(lmp, narg, arg) { rot_flag=true; } @@ -94,7 +94,7 @@ void ComputeTempUef::virial_rot(double *x, const double r[3][3]) // [00 10 20 ] [ 0 3 4 ] [00 01 02 ] // [01 11 21 ] [ 3 1 5 ] [10 11 12 ] // [02 12 22 ] [ 4 5 2 ] [20 21 22 ] - for (int k = 0; k<3; ++k) + for (int k = 0; k<3; ++k) { t[0][k] = x[0]*r[0][k] + x[3]*r[1][k] + x[4]*r[2][k]; t[1][k] = x[3]*r[0][k] + x[1]*r[1][k] + x[5]*r[2][k]; diff --git a/src/USER-UEF/compute_temp_uef.h b/src/USER-UEF/compute_temp_uef.h index 2e9dc901c0..460e2b18c0 100644 --- a/src/USER-UEF/compute_temp_uef.h +++ b/src/USER-UEF/compute_temp_uef.h @@ -1,4 +1,4 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov @@ -31,10 +31,10 @@ class ComputeTempUef : public ComputeTemp { ComputeTempUef(class LAMMPS *, int, char **); virtual ~ComputeTempUef(){} virtual void init(); - virtual void compute_vector(); + virtual void compute_vector(); void yes_rot(); void no_rot(); - + protected: bool rot_flag; @@ -55,6 +55,6 @@ only addition is: E: Can't use compute temp/uef without defining a fix nvt/npt/uef -Self-explanatory. +Self-explanatory. */ diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/USER-UEF/dump_cfg_uef.cpp index 44e1f8c5ae..4b0c08275a 100644 --- a/src/USER-UEF/dump_cfg_uef.cpp +++ b/src/USER-UEF/dump_cfg_uef.cpp @@ -36,8 +36,8 @@ enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCustom #define ONEFIELD 32 #define DELTA 1048576 -/* ---------------------------------------------------------------------- - * base method is mostly fine, just need to find the FixNHUef +/* ---------------------------------------------------------------------- + * base method is mostly fine, just need to find the FixNHUef * ----------------------------------------------------------------------*/ void DumpCFGUef::init_style() { @@ -58,7 +58,7 @@ void DumpCFGUef::init_style() ifix_uef=i; } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- * this is really the only difference between the base class and this one. * since the output is in scaled coordinates, changing the simulation box * edges to the flow frame will put coordinates in the flow frame too. diff --git a/src/USER-UEF/dump_cfg_uef.h b/src/USER-UEF/dump_cfg_uef.h index 059fc63008..d2881136ad 100644 --- a/src/USER-UEF/dump_cfg_uef.h +++ b/src/USER-UEF/dump_cfg_uef.h @@ -43,7 +43,7 @@ class DumpCFGUef : public DumpCFG { #endif /* ERROR/WARNING messages: - + E: Can't use dump cfg/uef without defining a fix nvt/npt/uef Self-explanatory. diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp index fe342f1efd..ee31674128 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -13,9 +13,9 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include "string.h" -#include "stdlib.h" -#include "math.h" +#include +#include +#include #include "fix_nh_uef.h" #include "atom.h" #include "force.h" diff --git a/src/USER-UEF/fix_npt_uef.cpp b/src/USER-UEF/fix_npt_uef.cpp index 1bf027bf85..b8ab1eccf9 100644 --- a/src/USER-UEF/fix_npt_uef.cpp +++ b/src/USER-UEF/fix_npt_uef.cpp @@ -13,14 +13,10 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include "string.h" #include "fix_npt_uef.h" -#include "modify.h" #include "error.h" using namespace LAMMPS_NS; -using namespace FixConst; - FixNPTUef::FixNPTUef(LAMMPS *lmp, int narg, char **arg) : FixNHUef(lmp, narg, arg) @@ -29,5 +25,4 @@ FixNPTUef::FixNPTUef(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Temperature control must be used with fix npt/uef"); if (!pstat_flag) error->all(FLERR,"Pressure control must be used with fix npt/uef"); - } diff --git a/src/USER-UEF/fix_npt_uef.h b/src/USER-UEF/fix_npt_uef.h index a77060a937..4c0cd28ae0 100644 --- a/src/USER-UEF/fix_npt_uef.h +++ b/src/USER-UEF/fix_npt_uef.h @@ -1,4 +1,4 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov diff --git a/src/USER-UEF/fix_nvt_uef.cpp b/src/USER-UEF/fix_nvt_uef.cpp index 589a4b5b56..2fd4a28545 100644 --- a/src/USER-UEF/fix_nvt_uef.cpp +++ b/src/USER-UEF/fix_nvt_uef.cpp @@ -13,14 +13,10 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include "string.h" #include "fix_nvt_uef.h" -#include "modify.h" #include "error.h" using namespace LAMMPS_NS; -using namespace FixConst; - FixNVTUef::FixNVTUef(LAMMPS *lmp, int narg, char **arg) : FixNHUef(lmp, narg, arg) @@ -29,7 +25,6 @@ FixNVTUef::FixNVTUef(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Temperature control must be used with fix nvt/uef"); if (pstat_flag) error->all(FLERR,"Pressure control can't be used with fix nvt/uef"); - } diff --git a/src/USER-UEF/fix_nvt_uef.h b/src/USER-UEF/fix_nvt_uef.h index a6eba7a284..718e36e756 100644 --- a/src/USER-UEF/fix_nvt_uef.h +++ b/src/USER-UEF/fix_nvt_uef.h @@ -1,4 +1,4 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov diff --git a/src/USER-UEF/uef_utils.cpp b/src/USER-UEF/uef_utils.cpp index 37ee896c7e..f270fe1d8b 100644 --- a/src/USER-UEF/uef_utils.cpp +++ b/src/USER-UEF/uef_utils.cpp @@ -11,20 +11,22 @@ See the README file in the top-level LAMMPS directory. Contributing author: David Nicholson (MIT) -------------------------------------------------------------------------- +------------------------------------------------------------------------- - This class contains functions to calculate the evolution of the periodic + This class contains functions to calculate the evolution of the periodic simulation box under elongational flow as described by Matthew Dobson in the arXiv preprint at http://arxiv.org/abs/1408.7078 - + Additionally, there are methods to do a lattice reduction to further reduce the simulation box using the method of Igor Semaev at http://link.springer.com/chapter/10.1007%2F3-540-44670-2_13 */ + #include #include "uef_utils.h" -namespace LAMMPS_NS{ namespace UEF_utils{ +namespace LAMMPS_NS { + namespace UEF_utils{ UEFBox::UEFBox() { @@ -46,7 +48,7 @@ UEFBox::UEFBox() // strain = w1 * theta1 + w2 * theta2 theta[0]=theta[1]=0; - + //set up the initial box l and change of basis matrix r for (int k=0;k<3;k++) for (int j=0;j<3;j++) @@ -124,8 +126,8 @@ void UEFBox::step_deform(const double ex, const double ey) theta[0] +=winv[0][0]*ex + winv[0][1]*ey; theta[1] +=winv[1][0]*ex + winv[1][1]*ey; - // deformation of the box. reduce() needs to - // be called regularly or calculation will become + // deformation of the box. reduce() needs to + // be called regularly or calculation will become // unstable double eps[3]; eps[0]=ex; eps[1] = ey; eps[2] = -ex-ey; @@ -148,7 +150,7 @@ bool UEFBox::reduce() theta[0] -= f1; theta[1] -= f2; - // store old change or basis matrix to determine if it + // store old change or basis matrix to determine if it // changes int r0[3][3]; for (int k=0;k<3;k++) @@ -157,7 +159,7 @@ bool UEFBox::reduce() // this modifies the old change basis matrix to // handle the case where the automorphism transforms - // the box but the reduced basis doesn't change + // the box but the reduced basis doesn't change // (r0 should still equal r at the end) if (f1 > 0) for (int k=0;k Date: Mon, 2 Oct 2017 17:19:42 -0400 Subject: [PATCH 12/21] small code refactor for FixNHUef class - use forward declaration for UEFBox to avoid having to include custom header - remove uef_arg_kludge() thanks to changes in 0c7879e9024309c54b5c5caf39c4b242b8e9e7b5 --- src/USER-UEF/fix_nh_uef.cpp | 186 ++++++++++++++---------------------- src/USER-UEF/fix_nh_uef.h | 10 +- 2 files changed, 77 insertions(+), 119 deletions(-) diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp index ee31674128..e2217daa82 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -34,69 +34,15 @@ #include "neighbor.h" #include "compute_pressure_uef.h" #include "compute_temp_uef.h" +#include "uef_utils.h" using namespace LAMMPS_NS; using namespace FixConst; enum{ISO,ANISO,TRICLINIC}; -/* ---------------------------------------------------------------------- - Put all of the uef-only keywords at the back of arg and make narg smaller - so FixNH::FixNH() only sees the keywords it knows. Save the numer of - remaining keywords in rem. - ---------------------------------------------------------------------- */ -char ** LAMMPS_NS::uef_arg_kludge(int &narg, char **arg, int &rem) -{ - int iarg = 3; - bool flags[3]= {false,false,false}; - rem=0; - char *tmp[3]; - while (iarg < narg) - { - if (strcmp(arg[iarg],"erate" ) == 0 && !flags[0]) - { - tmp[0] = arg[iarg]; - tmp[1] = arg[iarg+1]; - tmp[2] = arg[iarg+2]; - for (int k=iarg+3; kciteme) lmp->citeme->add(cite_user_uef_package); //initialization + erate[0] = erate[1] = 0; - //default values + + // default values + strain[0]=strain[1]= 0; ext_flags[0]=ext_flags[1]=ext_flags[2] = true; // need to initialize these + omega_dot[0]=omega_dot[1]=omega_dot[2]=0; - // parse remaining input + // parse fix nh/uef specific options + bool erate_flag = false; - int iarg = narg; - narg += rem; - while (iarg narg) error->all(FLERR,"Illegal fix nvt/npt/uef command"); erate[0] = force->numeric(FLERR,arg[iarg+1]); erate[1] = force->numeric(FLERR,arg[iarg+2]); erate_flag = true; iarg += 3; - } - else if (strcmp(arg[iarg],"strain")==0) { + } else if (strcmp(arg[iarg],"strain")==0) { if (iarg+3 > narg) error->all(FLERR,"Illegal fix nvt/npt/uef command"); strain[0] = force->numeric(FLERR,arg[iarg+1]); strain[1] = force->numeric(FLERR,arg[iarg+2]); iarg += 3; - } - else if (strcmp(arg[iarg],"ext")==0) { + } else if (strcmp(arg[iarg],"ext")==0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/uef command"); if (strcmp(arg[iarg+1],"x")==0) ext_flags[1] = ext_flags[2] = false; @@ -165,9 +113,10 @@ FixNHUef::FixNHUef(LAMMPS *lmp, int narg, char **arg) : iarg += 2; } - else - error->all(FLERR,"Illegal fix nvt/npt/uef command"); + // skip to next argument; argument check for unknown keywords is done in FixNH + ++iarg; } + if (!erate_flag) error->all(FLERR,"Keyword erate must be set for fix npt/npt/uef command"); @@ -176,7 +125,8 @@ FixNHUef::FixNHUef(LAMMPS *lmp, int narg, char **arg) : if (!domain->triclinic) error->all(FLERR,"Simulation box must be triclinic for fix/nvt/npt/uef"); - //check for conditions that impose a deviatoric stress + // check for conditions that impose a deviatoric stress + if (pstyle == TRICLINIC) error->all(FLERR,"Only normal stresses can be controlled with fix/nvt/npt/uef"); double erate_tmp[3]; @@ -184,43 +134,51 @@ FixNHUef::FixNHUef(LAMMPS *lmp, int narg, char **arg) : erate_tmp[1]=erate[1]; erate_tmp[2]=-erate[0]-erate[1]; - if (pstyle == ANISO) - { + if (pstyle == ANISO) { if (!(ext_flags[0] & ext_flags[1] & ext_flags[2])) error->all(FLERR,"The ext keyword may only be used with iso pressure control"); for (int k=0;k<3;k++) for (int j=0;j<3;j++) - if (p_flag[k] && p_flag[j]) - { + if (p_flag[k] && p_flag[j]) { double tol = 1e-6; - if ( !nearly_equal(p_start[k],p_start[j],tol) || !nearly_equal(p_stop[k],p_stop[j],tol)) - error->all(FLERR,"All controlled stresses must have the same value in fix/nvt/npt/uef"); - if ( !nearly_equal(erate_tmp[k],erate_tmp[j],tol) || !nearly_equal(erate_tmp[k],erate_tmp[j],tol)) - error->all(FLERR,"Dimensions with controlled stresses must have same strain rate in fix/nvt/npt/uef"); + if ( !nearly_equal(p_start[k],p_start[j],tol) + || !nearly_equal(p_stop[k],p_stop[j],tol)) + error->all(FLERR,"All controlled stresses must have the same " + "value in fix/nvt/npt/uef"); + if ( !nearly_equal(erate_tmp[k],erate_tmp[j],tol) + || !nearly_equal(erate_tmp[k],erate_tmp[j],tol)) + error->all(FLERR,"Dimensions with controlled stresses must have"\ + " same strain rate in fix/nvt/npt/uef"); } } - // conditions that produce a deviatoric stress have already - // been eliminated. + + // conditions that produce a deviatoric stress have already been eliminated. + deviatoric_flag=0; // need pre_exchange and irregular migration + pre_exchange_flag = 1; irregular = new Irregular(lmp); // flag that I change the box here (in case of nvt) + box_change_shape = 1; // initialize the UEFBox class which computes the box at each step + uefbox = new UEF_utils::UEFBox(); uefbox->set_strain(strain[0],strain[1]); - // reset fixedpoint to the stagnation point. I don't allow fixedpoint + // reset fixedpoint to the stagnation point. I don't allow fixedpoint // to be set by the user. + fixedpoint[0] = domain->boxlo[0]; fixedpoint[1] = domain->boxlo[1]; fixedpoint[2] = domain->boxlo[2]; - // Create temp and pressure computes for uef + // Create temp and pressure computes for nh/uef + int n = strlen(id) + 6; id_temp = new char[n]; strcpy(id_temp,id); @@ -232,6 +190,7 @@ FixNHUef::FixNHUef(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; tcomputeflag = 1; + n = strlen(id) + 7; id_press = new char[n]; strcpy(id_press,id); @@ -246,12 +205,10 @@ FixNHUef::FixNHUef(LAMMPS *lmp, int narg, char **arg) : pcomputeflag = 1; nevery = 1; - - } /* ---------------------------------------------------------------------- - * Erase the UEFBox object and get rid of the pressure compute if the nvt + * Erase the UEFBox object and get rid of the pressure compute if the nvt * version is being used. Everything else will be done in base destructor * ---------------------------------------------------------------------- */ FixNHUef::~FixNHUef() @@ -275,7 +232,7 @@ int FixNHUef::setmask() } /* ---------------------------------------------------------------------- - * Run FixNH::init() and do more error checking. Set the pressure + * Run FixNH::init() and do more error checking. Set the pressure * pointer in the case that the nvt version is used * ---------------------------------------------------------------------- */ void FixNHUef::init() @@ -294,19 +251,18 @@ void FixNHUef::init() // this will make the pressure compute for nvt if (!pstat_flag) - if (pcomputeflag) - { + if (pcomputeflag) { int icomp = modify->find_compute(id_press); if (icomp<0) error->all(FLERR,"Pressure ID for fix/nvt/uef doesn't exist"); pressure = modify->compute[icomp]; + if (strcmp(pressure->style,"pressure/uef") != 0) + error->all(FLERR,"Using fix nvt/npt/uef without a compute pressure/uef"); } - if (strcmp(pressure->style,"pressure/uef") != 0) - error->all(FLERR,"Using fix nvt/npt/uef without a compute pressure/uef"); + if (strcmp(temperature->style,"temp/uef") != 0) error->all(FLERR,"Using fix nvt/npt/uef without a compute temp/uef"); - } /* ---------------------------------------------------------------------- @@ -397,7 +353,7 @@ void FixNHUef::final_integrate_respa(int ilevel, int iloop) // outermost level - update eta_dot and omega_dot, apply via final_integrate // all other levels - NVE update of v if (ilevel == nlevels_respa-1) final_integrate(); - else + else { inv_rotate_v(rot); inv_rotate_f(rot); @@ -408,7 +364,7 @@ void FixNHUef::final_integrate_respa(int ilevel, int iloop) } /* ---------------------------------------------------------------------- - SLLOD velocity update in time-reversible (i think) increments + SLLOD velocity update in time-reversible (i think) increments v -> exp(-edot*dt/2)*v v -> v +f/m*dt v -> exp(-edot*dt/2)*v @@ -496,7 +452,7 @@ void FixNHUef::remap() } /* ---------------------------------------------------------------------- - SLLOD position update in time-reversible (i think) increments + SLLOD position update in time-reversible (i think) increments x -> exp(edot*dt/2)*x x -> x + v*dt x -> exp(edot*dt/2)*x @@ -590,11 +546,11 @@ void FixNHUef::pre_exchange() } } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- * The following are routines to rotate between the lab and upper triangular - * (UT) frames. For most of the time the simulation is in the UT frame. - * To get to the lab frame, apply the inv_rotate_[..](rot) and to - * get back to the UT frame apply rotate_[..](rot). + * (UT) frames. For most of the time the simulation is in the UT frame. + * To get to the lab frame, apply the inv_rotate_[..](rot) and to + * get back to the UT frame apply rotate_[..](rot). * * Note: the rotate_x() functions also apply a shift to/from the fixedpoint * to make the integration a little simpler. @@ -614,8 +570,8 @@ void FixNHUef::rotate_x(double r[3][3]) xn[0]=r[0][0]*x[i][0]+r[0][1]*x[i][1]+r[0][2]*x[i][2]; xn[1]=r[1][0]*x[i][0]+r[1][1]*x[i][1]+r[1][2]*x[i][2]; xn[2]=r[2][0]*x[i][0]+r[2][1]*x[i][1]+r[2][2]*x[i][2]; - x[i][0]=xn[0]+domain->boxlo[0]; - x[i][1]=xn[1]+domain->boxlo[1]; + x[i][0]=xn[0]+domain->boxlo[0]; + x[i][1]=xn[1]+domain->boxlo[1]; x[i][2]=xn[2]+domain->boxlo[2]; } } @@ -725,7 +681,7 @@ void FixNHUef::inv_rotate_f(double r[3][3]) } } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- * Increase the size of the restart list to add in the strains * ---------------------------------------------------------------------- */ int FixNHUef::size_restart_global() @@ -733,7 +689,7 @@ int FixNHUef::size_restart_global() return FixNH::size_restart_global() +2; } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- * Pack the strains after packing the default FixNH values * ---------------------------------------------------------------------- */ int FixNHUef::pack_restart_data(double *list) @@ -744,7 +700,7 @@ int FixNHUef::pack_restart_data(double *list) return n; } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- * read and set the strains after the default FixNH values * ---------------------------------------------------------------------- */ void FixNHUef::restart(char *buf) @@ -757,10 +713,10 @@ void FixNHUef::restart(char *buf) uefbox->set_strain(strain[0],strain[1]); } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- * If the step writes a restart, reduce the box beforehand. This makes sure * the unique box shape can be found once the restart is read and that - * all of the atoms lie within the box. + * all of the atoms lie within the box. * This may only be necessary for RESPA runs, but I'm leaving it in anyway. * ---------------------------------------------------------------------- */ void FixNHUef::end_of_step() @@ -780,9 +736,9 @@ void FixNHUef::end_of_step() } } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- * reduce the simulation box after a run is complete. otherwise it won't - * be possible to resume from a write_restart since the initialization of + * be possible to resume from a write_restart since the initialization of * the simulation box requires reduced simulation box * ---------------------------------------------------------------------- */ void FixNHUef::post_run() @@ -799,7 +755,7 @@ void FixNHUef::post_run() timer->stamp(Timer::NEIGH); } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- * public read for rotation matrix * ---------------------------------------------------------------------- */ void FixNHUef::get_rot(double r[3][3]) @@ -815,7 +771,7 @@ void FixNHUef::get_rot(double r[3][3]) r[2][2] = rot[2][2]; } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- * public read for ext flags * ---------------------------------------------------------------------- */ void FixNHUef::get_ext_flags(bool* e) @@ -825,7 +781,7 @@ void FixNHUef::get_ext_flags(bool* e) e[2] = ext_flags[2]; } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- * public read for simulation box * ---------------------------------------------------------------------- */ void FixNHUef::get_box(double b[3][3]) @@ -844,8 +800,8 @@ void FixNHUef::get_box(double b[3][3]) b[2][2] = box[2][2]; } -/* ---------------------------------------------------------------------- - * comparing floats +/* ---------------------------------------------------------------------- + * comparing floats * it's imperfect, but should work provided no infinities * ---------------------------------------------------------------------- */ bool FixNHUef::nearly_equal(double a, double b, double epsilon) diff --git a/src/USER-UEF/fix_nh_uef.h b/src/USER-UEF/fix_nh_uef.h index 8b0f07a34b..43f5bb46a9 100644 --- a/src/USER-UEF/fix_nh_uef.h +++ b/src/USER-UEF/fix_nh_uef.h @@ -1,4 +1,4 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator www.cs.sandia.gov/~sjplimp/lammps.html Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories @@ -17,12 +17,14 @@ #ifndef LMP_FIX_NH_UEF_H #define LMP_FIX_NH_UEF_H -#include "uef_utils.h" #include "fix_nh.h" namespace LAMMPS_NS { + // forward declaration + namespace UEF_utils { + class UEFBox; + }; -char **uef_arg_kludge(int&, char**, int&); class FixNHUef : public FixNH { public: FixNHUef(class LAMMPS *, int, char **); @@ -59,7 +61,7 @@ class FixNHUef : public FixNH { int rem; //this is for the narg kluge - UEF_utils::UEFBox *uefbox; // interface for the special simulation box + UEF_utils::UEFBox *uefbox; // interface for the special simulation box double rot[3][3]; // rotation matrix bool ext_flags[3]; // flags for external "free surfaces" From 8acdc8020d9a548266795dbcb91a43e0c4378a3c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 2 Oct 2017 17:24:36 -0400 Subject: [PATCH 13/21] add USER-UEF classes to .gitignore --- src/.gitignore | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/.gitignore b/src/.gitignore index 1571065b72..8fe732ece6 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -103,6 +103,15 @@ /sna.cpp /sna.h +/uef_*.cpp +/uef_*.h +/compute_*uef.cpp +/compute_*uef.h +/dump_*uef.cpp +/dump_*uef.h +/fix_*uef.cpp +/fix_*uef.h + /atom_vec_wavepacket.cpp /atom_vec_wavepacket.h /fix_nve_awpmd.cpp From 92d9b361fcda759ed72944cf92dbc07f8e0e9b84 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 2 Oct 2017 17:39:59 -0400 Subject: [PATCH 14/21] include USER-UEF styles in PDF version of manual --- doc/src/lammps.book | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 86dfe78af3..77c70775d7 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -62,6 +62,7 @@ dump_modify.html dump_molfile.html dump_netcdf.html dump_vtk.html +dump_cfg_uef.html echo.html fix.html fix_modify.html @@ -231,6 +232,7 @@ fix_nvt_manifold_rattle.html fix_nvt_sllod.html fix_nvt_sllod_eff.html fix_nvt_sphere.html +fix_nh_uef.html fix_oneway.html fix_orient.html fix_phonon.html @@ -354,6 +356,7 @@ compute_pe.html compute_pe_atom.html compute_plasticity_atom.html compute_pressure.html +compute_pressure_uef.html compute_property_atom.html compute_property_chunk.html compute_property_local.html @@ -403,6 +406,7 @@ compute_temp_region.html compute_temp_region_eff.html compute_temp_rotate.html compute_temp_sphere.html +compute_temp_uef.html compute_ti.html compute_torque_chunk.html compute_vacf.html From 00aef0fe00141d8cb17b365bc51859755249f991 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 2 Oct 2017 17:40:46 -0400 Subject: [PATCH 15/21] rerun logfiles for USER-UEF example inputs --- .../npt_biaxial/log.22Sep17.npt_biaxial.g++.1 | 430 ++++++++--------- .../npt_biaxial/log.22Sep17.npt_biaxial.g++.4 | 438 +++++++++--------- .../log.22Sep17.npt_uniaxial.g++.1 | 281 ++++++++++- .../log.22Sep17.npt_uniaxial.g++.4 | 402 ++++++++-------- 4 files changed, 915 insertions(+), 636 deletions(-) diff --git a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1 b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1 index 12de8ff8be..7ef4482b9d 100644 --- a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1 +++ b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1 @@ -52,233 +52,233 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 2.742 | 2.742 | 2.742 Mbytes Step c_1_press[1] c_1_press[2] c_1_press[3] 0 6.3937851 7.0436438 6.4461087 - 50 7.9020345 7.303289 14.733929 - 100 8.3214325 8.385843 13.166247 - 150 5.7168419 5.6083988 9.7224198 - 200 3.8875348 4.0840705 7.9912973 - 250 4.2933724 4.2410519 7.7200953 - 300 4.5452314 4.2434949 8.6709832 - 350 5.446489 5.6166962 11.300536 - 400 6.0682558 5.7787878 12.106852 - 450 5.3884296 5.5066688 9.9100012 - 500 4.8046418 4.7115986 9.9769201 - 550 4.9043933 4.6240966 9.319336 - 600 4.6843238 4.9571246 9.5325487 - 650 5.1952989 5.195648 9.6187047 - 700 5.4163364 5.2938289 10.136655 - 750 5.6723178 5.0670261 11.415221 - 800 5.9379901 5.6402916 10.815209 - 850 5.0695389 5.3021432 10.742859 - 900 4.6498962 4.7111912 9.8453523 - 950 4.4811641 5.170132 9.421765 - 1000 4.7501483 4.2420772 9.3510803 - 1050 4.5973379 5.2046799 9.8632975 - 1100 4.7879562 4.9051316 9.8658626 - 1150 5.0528771 5.5048545 10.110913 - 1200 4.9926563 5.2482081 9.9610863 - 1250 4.8476232 4.8498859 9.5752989 - 1300 5.2932038 5.0594534 10.869545 - 1350 5.4720421 5.0830442 10.69386 - 1400 4.8175566 4.9863651 10.041898 - 1450 4.6307145 4.5615459 9.231299 - 1500 5.0296259 4.5433558 8.7180513 - 1550 4.8708444 5.1601014 10.256791 - 1600 5.5098593 5.316773 10.224386 - 1650 5.5055907 5.0516814 10.272037 - 1700 4.6965552 5.2436628 9.8272905 - 1750 5.0212307 4.740601 8.9738802 - 1800 4.7756351 5.199734 9.9929449 - 1850 4.7107092 5.177203 10.580427 - 1900 5.0935608 4.5286844 9.3036832 - 1950 4.8035855 4.894359 9.4423987 - 2000 4.5643937 4.7480477 9.4384251 - 2050 4.9314701 4.990414 10.151815 - 2100 5.9828824 5.8188026 12.262691 - 2150 5.5337303 5.4598468 10.136112 - 2200 4.892172 4.8699674 9.1629905 - 2250 4.5680591 4.5740533 9.5633545 - 2300 5.0023535 4.3948659 8.9645774 - 2350 5.2533056 4.9803884 10.255653 - 2400 5.3330196 5.3888322 10.021617 - 2450 5.2095527 4.8765336 10.135381 - 2500 5.221153 5.2974568 10.2493 - 2550 5.385331 5.0801192 10.490479 - 2600 5.3274988 5.0253548 10.147587 - 2650 4.718677 5.2710337 9.7549521 - 2700 4.5811521 4.6083971 8.1923164 - 2750 4.4743752 4.3319737 8.8690805 - 2800 5.0215013 5.2262961 9.8627954 - 2850 6.1005107 5.5994942 11.170661 - 2900 5.9673524 5.362124 10.401699 - 2950 5.5400849 5.7523993 10.292536 - 3000 4.9202636 5.1210431 10.125839 - 3050 4.5286487 5.3586164 9.8634322 - 3100 4.5719961 5.1615414 9.8027972 - 3150 5.4091919 4.8581943 9.96938 - 3200 5.522125 5.3564838 9.7638407 - 3250 4.9019062 5.2514758 9.2993079 - 3300 5.2375918 5.1439012 9.4313575 - 3350 4.750235 4.8692016 10.54193 - 3400 5.5793211 5.4184157 11.021389 - 3450 4.9022614 5.3166498 9.4629659 - 3500 4.6348617 4.4650979 9.0665548 - 3550 4.7922405 4.8961269 10.255446 - 3600 4.8914457 5.1158894 9.4736084 - 3650 5.062771 4.6725475 10.263484 - 3700 5.4842823 5.7793971 10.342915 - 3750 5.3136012 5.063065 10.398307 - 3800 4.9372149 4.9270414 9.5304748 - 3850 5.2144752 5.1716455 9.7575725 - 3900 5.0892665 5.1697057 9.918052 - 3950 5.1124507 5.354702 9.791366 - 4000 5.1255084 5.1143653 10.913101 - 4050 5.1891698 4.9913681 9.6871728 - 4100 4.7663368 4.2435014 8.3815668 - 4150 4.8060033 4.3415868 9.6553386 - 4200 4.8548303 4.8006768 9.5995801 - 4250 5.0976366 5.2683175 10.386444 - 4300 5.8921937 5.5134696 10.788143 - 4350 5.8323871 5.5255869 11.199128 - 4400 5.2464655 5.0005905 10.311055 - 4450 4.9264849 5.2499854 10.26702 - 4500 4.4431895 4.536981 8.7489096 - 4550 4.5180914 4.2080277 8.6525529 - 4600 5.1782188 5.1224059 10.683341 - 4650 5.4156233 4.8714464 10.473939 - 4700 5.3107669 5.224614 10.569391 - 4750 4.9538022 5.2509475 10.288918 - 4800 4.6976945 4.8107142 9.8299772 - 4850 5.1227936 5.0737571 10.440452 - 4900 4.7580514 4.6375995 9.1971008 - 4950 5.0647601 4.6470735 9.583131 - 5000 5.196231 5.7531491 10.409807 - 5050 5.6691323 5.7163652 12.335701 - 5100 5.3603738 5.4887106 10.961712 - 5150 4.455028 4.6494465 9.8096968 - 5200 4.7596912 4.4804896 9.3762885 - 5250 5.3144927 5.0113772 9.553101 - 5300 5.3445266 4.8262035 9.1220802 - 5350 5.1540657 5.5982676 10.765178 - 5400 5.1773418 5.2684381 10.452351 - 5450 4.8946859 5.3283747 9.8015564 - 5500 5.2009608 4.7183522 9.4558009 - 5550 5.4158589 5.5005458 10.539505 - 5600 4.7196831 5.4181991 9.6439249 - 5650 4.8333571 4.8601728 8.9350189 - 5700 5.4395698 4.9730096 10.669681 - 5750 5.2947443 5.6973259 10.020539 - 5800 5.4391993 5.5255143 10.264969 - 5850 4.9921388 5.2643827 10.217028 - 5900 5.0048643 4.7952641 8.9718929 - 5950 5.1843818 4.5987295 9.6858944 - 6000 5.0343993 4.946933 9.7436708 - 6050 4.6202714 5.3502658 10.752915 - 6100 5.6914422 5.3621964 10.281827 - 6150 5.1928763 5.9652686 10.923881 - 6200 5.0030409 5.2013891 10.056308 - 6250 4.9699876 5.2363753 9.9964211 - 6300 4.9129606 4.4558458 9.0419952 - 6350 4.6623958 4.4078264 8.528649 - 6400 4.9811441 5.1183207 10.261751 - 6450 5.3644017 5.5153937 10.401295 - 6500 5.6674981 5.7427566 11.928777 - 6550 5.1622364 5.3212928 10.067198 - 6600 4.5954278 5.1645397 10.16724 - 6650 4.9192712 5.0413326 9.95656 - 6700 4.6179845 4.5656214 9.3798952 - 6750 4.7287495 4.5071148 8.7890116 - 6800 4.8600442 4.8083512 10.245595 - 6850 5.0515531 5.1609272 10.553855 - 6900 5.1159742 5.1359869 10.594699 - 6950 4.8908884 5.0592418 9.5698704 - 7000 4.7654136 4.7530776 8.9439321 - 7050 4.779293 4.7534957 9.7244349 - 7100 5.2265831 5.6869073 10.32717 - 7150 5.4019177 5.15174 10.457567 - 7200 4.9817102 5.0596098 10.337574 - 7250 5.1836654 5.6065238 10.723108 - 7300 4.2916569 4.457143 8.5419099 - 7350 4.3906104 4.5439294 9.0805415 - 7400 4.998572 5.3386063 10.491418 - 7450 5.1109022 5.0506801 10.636116 - 7500 5.0248381 5.019932 10.217023 - 7550 5.0109265 5.1438717 9.9032426 - 7600 4.6628614 4.6204146 8.9459669 - 7650 4.8930717 5.0650009 10.049331 - 7700 4.9373454 5.6265835 10.210644 - 7750 5.5001067 5.3133253 10.667995 - 7800 5.0816102 5.0125753 10.591986 - 7850 4.9638046 5.1969015 9.9728333 - 7900 4.8438207 4.9217213 8.9978809 - 7950 4.7318805 4.6248537 8.6806596 - 8000 5.2808543 5.2892613 10.932535 - 8050 5.9609722 5.87087 10.47602 - 8100 5.2190231 5.6693244 11.244536 - 8150 5.3481127 5.2849903 10.222845 - 8200 4.7833053 4.7404657 9.2034474 - 8250 4.5461994 4.510467 10.294452 - 8300 4.6025175 4.8332817 8.7967546 - 8350 5.0389897 5.6642908 10.243402 - 8400 4.8414338 4.8925143 9.3653631 - 8450 5.5087429 4.7830361 10.831666 - 8500 5.2678146 5.1697789 9.9105782 - 8550 5.1211843 4.9097801 9.4165956 - 8600 5.8239149 5.0821022 10.803261 - 8650 5.3620154 5.5831747 11.16202 - 8700 5.1625813 4.8791404 10.537681 - 8750 4.5622461 5.0157549 10.013227 - 8800 4.4051517 5.0224553 9.6364273 - 8850 4.1711629 4.635617 8.5470244 - 8900 4.7049907 5.2458435 10.100728 - 8950 4.8568883 5.2360772 9.2306469 - 9000 5.0091899 5.2203574 10.718541 - 9050 5.1037824 4.9022451 10.24271 - 9100 5.0789015 4.9331454 9.173614 - 9150 5.3865455 5.3427553 11.40199 - 9200 5.5089482 5.9423232 10.976063 - 9250 5.1353552 5.0650262 10.040607 - 9300 4.6761948 4.9155175 9.6413722 - 9350 4.4780834 4.3934708 8.7049819 - 9400 4.2561799 4.7906324 9.046134 - 9450 5.6162819 5.2881846 9.9040868 - 9500 5.7554547 5.6111262 10.23849 - 9550 5.4230462 5.5656045 10.908006 - 9600 5.5045685 4.9818892 9.8929535 - 9650 5.0541481 5.0183351 9.5226021 - 9700 4.9712829 5.2395398 9.9996693 - 9750 5.0960017 5.4419775 10.914719 - 9800 5.0790688 5.6378474 10.00789 - 9850 4.9661747 5.114502 9.4585052 - 9900 5.0133498 4.7456254 9.4572653 - 9950 5.3318846 4.6643122 10.096292 - 10000 5.2227687 4.8924305 9.5894615 -Loop time of 4.5628 on 1 procs for 10000 steps with 500 atoms + 50 8.656807 7.9950197 15.884241 + 100 11.492654 12.329741 17.658703 + 150 8.6981119 8.6206624 14.114117 + 200 6.1456927 6.4457399 11.199275 + 250 5.5832485 5.5648091 10.400142 + 300 6.1328799 6.3010248 12.010437 + 350 7.1731722 7.5434426 14.588724 + 400 9.3347098 8.6490053 16.710495 + 450 9.5796766 8.9745197 18.230488 + 500 8.4810279 7.6334377 15.050771 + 550 6.5621497 7.401369 12.711355 + 600 6.5868791 6.4912059 13.361745 + 650 7.8188208 7.1180707 14.27939 + 700 7.6714427 7.8664221 14.845323 + 750 7.1545213 8.1596642 14.255973 + 800 8.1950866 8.6441652 15.642584 + 850 8.5624855 8.4004152 15.303218 + 900 7.2513729 7.5226938 12.951415 + 950 6.9147541 7.4166796 13.712136 + 1000 7.9356665 7.9447497 14.787789 + 1050 8.0049947 8.3262124 15.736553 + 1100 7.4778576 7.8850531 15.063925 + 1150 7.5982598 7.3264091 14.300757 + 1200 7.7140371 7.2955688 14.347757 + 1250 7.4219774 7.0057022 13.701556 + 1300 8.0349765 7.8954305 14.361289 + 1350 7.6041533 8.1862555 15.296344 + 1400 7.7416819 7.7959914 15.162316 + 1450 8.0188314 7.2866705 14.983598 + 1500 7.4473216 7.3994359 14.067676 + 1550 7.8852675 7.3618461 14.061472 + 1600 7.7365655 7.5982634 14.68822 + 1650 8.3347522 8.1032999 16.189298 + 1700 8.021765 7.6018364 14.337751 + 1750 6.8819319 6.5380502 13.166309 + 1800 6.6099094 6.915077 12.331541 + 1850 7.4163951 7.8158695 14.534615 + 1900 8.4061445 8.3757582 15.887245 + 1950 8.1452338 8.4887365 15.059168 + 2000 8.6938353 9.0101284 16.680096 + 2050 7.4587753 7.7917795 15.211311 + 2100 7.0551172 7.110128 14.141606 + 2150 7.0175122 6.6961241 14.279182 + 2200 6.9961187 7.3322415 13.171629 + 2250 7.5170372 7.2002508 13.655891 + 2300 7.5550073 7.889281 15.268156 + 2350 8.6343715 8.1446746 15.343131 + 2400 7.8734662 8.2266284 15.094857 + 2450 8.4135272 8.7207275 16.025335 + 2500 7.2176413 7.863538 16.295816 + 2550 8.1745427 8.093571 14.982008 + 2600 7.3905296 7.033819 13.473161 + 2650 6.7049957 6.4518564 13.109849 + 2700 7.0979639 7.2722444 13.108017 + 2750 8.013824 7.9399712 14.221876 + 2800 8.4370721 8.6814371 16.44629 + 2850 7.8347153 8.1521156 15.561372 + 2900 8.035115 7.8964336 14.867854 + 2950 7.1672845 7.3532206 15.440881 + 3000 7.5346666 6.9003742 14.27777 + 3050 7.3784203 7.3252438 14.047681 + 3100 7.2587022 6.9154856 13.171992 + 3150 7.2711856 7.7599218 15.241926 + 3200 8.5378786 8.4297377 15.866421 + 3250 8.0342828 8.0687328 15.416609 + 3300 7.5984747 7.2012637 13.601468 + 3350 7.3021124 6.9641186 12.646778 + 3400 7.209707 7.8050641 14.085147 + 3450 7.5112359 7.7338405 15.677763 + 3500 8.8355621 8.8289163 16.331319 + 3550 7.9119042 8.47938 14.393274 + 3600 7.4370847 7.2492674 14.933099 + 3650 7.2371175 7.2652477 13.586608 + 3700 7.172453 6.5367899 14.64114 + 3750 7.3950889 7.1264975 14.372124 + 3800 7.7074509 7.5716747 14.839055 + 3850 7.8509762 8.1926443 15.486783 + 3900 8.0742138 7.8584144 14.887115 + 3950 6.9346973 7.8694823 14.666153 + 4000 7.6621984 7.6382651 14.793905 + 4050 7.4090172 7.3118869 14.993099 + 4100 7.6033087 8.3890976 15.461012 + 4150 8.0450732 8.2172794 16.263521 + 4200 7.1723176 6.8215613 12.761291 + 4250 7.1840793 7.219089 14.163744 + 4300 7.1380776 7.5355394 14.487621 + 4350 7.6523602 7.7530752 15.549788 + 4400 7.9503171 8.0947449 15.058755 + 4450 7.5850837 7.5248838 15.796171 + 4500 7.1597196 7.0346482 13.889614 + 4550 7.5588017 7.4473311 14.513886 + 4600 7.1855439 7.7743654 13.928596 + 4650 7.8936012 8.0911603 15.821516 + 4700 7.5437461 8.4762734 15.249242 + 4750 7.5999136 8.0141389 14.942225 + 4800 7.6708678 7.4003145 13.855277 + 4850 7.5902038 7.0718185 14.676038 + 4900 7.6448398 7.7623026 15.013123 + 4950 8.1761651 8.2132532 15.827257 + 5000 7.5310459 7.9710358 14.570133 + 5050 7.3910867 7.9090596 14.644752 + 5100 7.5096472 8.0032554 14.151557 + 5150 7.4930298 7.6627654 14.776418 + 5200 8.0258893 6.9808848 14.80221 + 5250 7.621093 7.5081066 14.18567 + 5300 7.7724131 7.3547437 13.390993 + 5350 7.7141018 7.4182737 15.383453 + 5400 7.5798525 7.604214 13.772184 + 5450 8.1532137 7.7843706 15.636038 + 5500 8.0049611 7.79693 14.435558 + 5550 8.2449821 7.9493856 15.227616 + 5600 8.3248504 7.6677271 14.929828 + 5650 7.7005024 7.8412131 14.508952 + 5700 7.3062546 7.3272456 13.075895 + 5750 7.2476367 7.1095473 14.729012 + 5800 8.302566 8.358882 14.667741 + 5850 8.3481651 7.7985514 15.305433 + 5900 6.6533193 7.1150305 13.497761 + 5950 7.2385939 7.9132287 14.889887 + 6000 7.5594171 7.7167581 14.878921 + 6050 7.5977124 7.583702 15.842984 + 6100 8.1433134 8.1548274 15.253848 + 6150 7.4371297 7.7036444 13.892215 + 6200 7.3807114 7.2270114 14.32622 + 6250 7.5101996 6.7835902 14.62525 + 6300 7.779059 7.0241215 14.008402 + 6350 7.7217303 7.8795697 14.544095 + 6400 8.0987528 8.2649512 15.615863 + 6450 7.5662457 7.4332335 14.174783 + 6500 7.3672018 7.691987 13.757496 + 6550 7.4424935 7.4401054 14.660643 + 6600 8.0670938 8.4028068 15.558513 + 6650 7.9428662 7.5886468 15.814302 + 6700 7.5792547 7.5877961 14.300332 + 6750 6.6732262 7.5855672 14.322929 + 6800 7.2340735 7.6129085 13.010849 + 6850 7.3530804 7.2093837 14.012405 + 6900 8.1335803 8.1621205 14.290907 + 6950 8.0140455 8.0254163 15.242386 + 7000 7.9944794 8.1150205 15.343835 + 7050 7.6449634 8.4930222 16.254105 + 7100 8.1486038 7.5521474 14.659373 + 7150 6.9146032 7.1979211 13.220697 + 7200 7.1472024 6.8585436 13.747498 + 7250 7.0570799 7.1226848 13.576252 + 7300 7.5713738 7.5064849 14.195069 + 7350 8.6995152 8.4776231 15.983028 + 7400 8.0043956 8.3894875 16.583907 + 7450 7.6606913 7.6695256 13.758723 + 7500 6.925632 7.1358864 13.882849 + 7550 7.284765 7.4400093 12.797499 + 7600 7.1815013 7.0465795 14.661597 + 7650 9.0926556 8.6982979 16.243272 + 7700 9.0289976 8.2542699 15.359908 + 7750 7.6042308 7.350186 15.701097 + 7800 7.7931461 7.5777572 14.397664 + 7850 6.9603382 6.7910235 14.020762 + 7900 7.0994051 6.7555761 13.020541 + 7950 7.4253662 7.0888087 15.177881 + 8000 8.0943311 8.5234668 15.990661 + 8050 7.8770545 8.1329374 14.434819 + 8100 7.114341 7.9621662 15.488984 + 8150 7.6483959 7.7800045 14.790885 + 8200 6.8915301 7.4275666 14.360578 + 8250 6.8943728 7.4597132 13.852787 + 8300 7.5013271 8.0231338 14.983933 + 8350 7.285471 7.5175898 15.318651 + 8400 8.0954536 8.3126472 15.494494 + 8450 7.7122605 7.4228532 15.422058 + 8500 8.0793058 7.077081 14.736069 + 8550 7.1928433 6.8056774 13.691643 + 8600 7.0377566 7.3074361 14.141988 + 8650 7.3824217 7.4739032 14.679069 + 8700 7.7684482 8.1554503 15.191035 + 8750 7.9590885 8.1135479 14.338724 + 8800 8.1231133 7.7860088 15.403904 + 8850 8.5000448 8.1024052 15.173116 + 8900 7.3845853 7.9495964 14.619746 + 8950 7.5818306 7.2248015 14.621207 + 9000 7.2164673 6.6633348 15.609622 + 9050 7.5851603 8.0836264 15.022988 + 9100 7.8771779 7.6350639 14.077462 + 9150 7.6077035 6.8475422 14.315993 + 9200 7.6583735 7.5077759 14.569883 + 9250 7.5263046 7.7028057 14.57854 + 9300 7.2162602 8.053893 16.02041 + 9350 8.3756477 8.1996826 14.70403 + 9400 7.7634122 7.5041574 13.936959 + 9450 7.3067071 7.7438443 14.542518 + 9500 7.4048127 7.44049 14.821218 + 9550 7.2884669 7.9974016 14.367535 + 9600 7.4198667 7.9510424 15.713394 + 9650 7.9099018 8.0161955 15.006711 + 9700 7.3372719 7.419692 14.320242 + 9750 7.2075957 7.3109181 14.541501 + 9800 7.6617849 7.7279899 15.018225 + 9850 7.6595385 7.138483 14.400928 + 9900 7.1440851 7.3065973 12.81291 + 9950 7.5757356 7.3889652 14.59353 + 10000 8.5866601 8.347723 16.125389 +Loop time of 3.74766 on 1 procs for 10000 steps with 500 atoms -Performance: 946786.828 tau/day, 2191.636 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1152718.368 tau/day, 2668.330 timesteps/s +99.4% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.70711 | 0.70711 | 0.70711 | 0.0 | 15.50 -Neigh | 2.7689 | 2.7689 | 2.7689 | 0.0 | 60.69 -Comm | 0.30715 | 0.30715 | 0.30715 | 0.0 | 6.73 -Output | 0.0036616 | 0.0036616 | 0.0036616 | 0.0 | 0.08 -Modify | 0.67113 | 0.67113 | 0.67113 | 0.0 | 14.71 -Other | | 0.1048 | | | 2.30 +Pair | 0.64903 | 0.64903 | 0.64903 | 0.0 | 17.32 +Neigh | 2.2534 | 2.2534 | 2.2534 | 0.0 | 60.13 +Comm | 0.22293 | 0.22293 | 0.22293 | 0.0 | 5.95 +Output | 0.0034931 | 0.0034931 | 0.0034931 | 0.0 | 0.09 +Modify | 0.53533 | 0.53533 | 0.53533 | 0.0 | 14.28 +Other | | 0.08346 | | | 2.23 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 905 ave 905 max 905 min +Nghost: 919 ave 919 max 919 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3340 ave 3340 max 3340 min +Neighs: 3662 ave 3662 max 3662 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 3340 -Ave neighs/atom = 6.68 -Neighbor list builds = 4580 +Total # of neighbors = 3662 +Ave neighs/atom = 7.324 +Neighbor list builds = 4480 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:04 +Total wall time: 0:00:03 diff --git a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 index 7a2c553fcf..2e2d9989dd 100644 --- a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 +++ b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 @@ -52,233 +52,233 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 2.71 | 2.71 | 2.71 Mbytes Step c_1_press[1] c_1_press[2] c_1_press[3] 0 6.3937851 7.0436438 6.4461087 - 50 7.9020345 7.303289 14.733929 - 100 8.3214325 8.385843 13.166247 - 150 5.7168419 5.6083988 9.7224198 - 200 3.8875348 4.0840705 7.9912973 - 250 4.2933724 4.2410519 7.7200953 - 300 4.5452314 4.2434949 8.6709832 - 350 5.446489 5.6166962 11.300536 - 400 6.0682558 5.7787878 12.106852 - 450 5.3884296 5.5066688 9.9100012 - 500 4.8046418 4.7115986 9.9769201 - 550 4.9043933 4.6240966 9.319336 - 600 4.6843238 4.9571246 9.5325487 - 650 5.1952989 5.195648 9.6187047 - 700 5.4163364 5.2938289 10.136655 - 750 5.6723178 5.0670261 11.415221 - 800 5.9379901 5.6402916 10.815209 - 850 5.0695389 5.3021432 10.742859 - 900 4.6498961 4.7111912 9.8453525 - 950 4.4811637 5.1701321 9.4217645 - 1000 4.750149 4.2420768 9.3510788 - 1050 4.5973376 5.2046787 9.8633025 - 1100 4.7879516 4.9051338 9.8658577 - 1150 5.0528775 5.5048673 10.110905 - 1200 4.992684 5.2482046 9.9610521 - 1250 4.8475843 4.8499105 9.575365 - 1300 5.2930179 5.0593567 10.869332 - 1350 5.4722311 5.0830422 10.69342 - 1400 4.8165864 4.9851485 10.042141 - 1450 4.6276548 4.5643142 9.2306057 - 1500 5.0197119 4.5470582 8.7204541 - 1550 4.878215 5.158312 10.264148 - 1600 5.4917782 5.3121766 10.273923 - 1650 5.4381825 5.1698438 9.9823968 - 1700 4.9206398 5.2852701 9.5806048 - 1750 4.9226742 4.7164231 8.932911 - 1800 4.9733613 4.8776709 9.6638069 - 1850 5.1327098 4.8503755 10.170281 - 1900 5.9114024 6.0045781 10.515973 - 1950 5.2332897 5.7899133 10.436353 - 2000 5.286098 5.3874673 10.124669 - 2050 5.0167541 5.490974 9.6476751 - 2100 5.3933017 5.372036 9.7187857 - 2150 4.8288683 4.7937794 9.2252452 - 2200 5.0760371 4.8515447 9.8373704 - 2250 5.5626387 5.5509581 10.274505 - 2300 5.1009883 4.9400598 10.300516 - 2350 5.3148808 5.4689154 9.9240269 - 2400 4.8720251 4.9341152 10.32893 - 2450 5.1964062 5.394913 9.6729737 - 2500 4.9715986 5.1500527 10.925999 - 2550 5.1240848 4.3358732 9.9783677 - 2600 4.7387276 4.3732544 9.4545219 - 2650 4.6787161 4.7001729 9.4697272 - 2700 5.5549736 5.4437977 10.581898 - 2750 5.523176 5.0416156 10.338311 - 2800 5.3864512 5.439205 10.079435 - 2850 5.5675261 5.2310133 10.524415 - 2900 5.2628013 5.3641439 10.160587 - 2950 4.7300407 4.6838026 8.9617691 - 3000 5.1744361 4.5005726 10.487918 - 3050 5.2239211 5.3030573 10.376913 - 3100 5.1016236 5.0700451 9.4697833 - 3150 5.0661402 5.142376 9.5591223 - 3200 5.397775 4.9229072 10.389504 - 3250 5.5515257 5.2365437 10.265586 - 3300 5.844715 5.2552463 10.065811 - 3350 4.888658 5.0636003 10.129015 - 3400 4.55264 5.0703435 8.7178922 - 3450 4.992088 5.2487278 10.087295 - 3500 5.3469913 4.785277 9.8944509 - 3550 5.217282 5.3011196 9.6306807 - 3600 5.8928519 4.9717327 10.897022 - 3650 6.0118006 5.9046823 11.2352 - 3700 5.0667885 5.2572827 10.266895 - 3750 4.8133435 4.8991016 9.4760522 - 3800 4.5125756 4.8295067 9.0226716 - 3850 4.4651224 4.678168 8.7474636 - 3900 4.9811965 4.687682 9.0547397 - 3950 5.2387906 5.4772104 10.416997 - 4000 5.3576384 5.896421 10.524538 - 4050 5.8265842 5.7449599 10.527804 - 4100 5.2276111 5.1866643 10.1139 - 4150 5.2739201 4.8869905 9.5700647 - 4200 4.7943987 4.4305245 8.8436208 - 4250 4.9285996 4.9591754 10.121985 - 4300 5.5289613 6.0688348 10.898698 - 4350 5.6673111 5.3636174 10.569902 - 4400 4.7882862 5.3060196 10.050009 - 4450 5.1309456 4.9776646 9.8804906 - 4500 5.0629205 4.7277565 8.7584435 - 4550 5.1009496 4.8110658 9.4666416 - 4600 5.5858872 5.4123191 12.263621 - 4650 5.5585654 5.8537188 10.258869 - 4700 4.8064416 5.060519 10.153314 - 4750 4.7181218 5.0631685 9.3624778 - 4800 4.871496 4.8872111 9.7435175 - 4850 4.8297469 4.6464864 9.6852358 - 4900 5.5682142 5.5530971 10.073983 - 4950 5.1322491 5.3402989 10.283117 - 5000 5.4516954 5.6198027 11.223665 - 5050 5.1488128 5.1092478 10.375804 - 5100 4.4000207 4.7355267 9.5152048 - 5150 4.6501804 5.0426405 9.5383808 - 5200 4.8589325 4.9719089 8.8114996 - 5250 5.0343815 4.8677968 10.967149 - 5300 5.6710156 5.5661349 11.436985 - 5350 5.2243912 5.101865 9.9427717 - 5400 4.3337053 4.6325695 9.6917273 - 5450 4.6217314 5.0129144 9.1988349 - 5500 5.1014594 4.7848497 10.516995 - 5550 5.0465061 4.9173385 9.3561229 - 5600 4.8643636 4.860697 10.428496 - 5650 5.6536439 5.4434563 10.014098 - 5700 4.9734376 4.7193345 9.5610177 - 5750 5.3414745 5.148175 11.048378 - 5800 5.4363776 5.0286279 10.85538 - 5850 5.1060233 5.1350774 9.3190058 - 5900 4.5611096 4.4980661 8.8914749 - 5950 4.4264357 4.7757911 8.4601102 - 6000 5.059237 5.6791366 10.779186 - 6050 5.3216769 5.8043231 10.290497 - 6100 5.0261845 5.3700963 10.430661 - 6150 5.8132491 5.5245642 10.675176 - 6200 5.2346131 5.21174 10.332249 - 6250 5.3756188 4.787094 9.7496811 - 6300 5.2054751 4.7341501 10.034542 - 6350 5.1908834 4.9041004 9.2702025 - 6400 4.2876866 4.3860725 9.3793733 - 6450 5.1264657 4.8049065 9.9620589 - 6500 5.019625 5.4901247 9.821544 - 6550 5.3251841 5.3680612 10.021716 - 6600 5.2494437 4.8680991 9.5942134 - 6650 5.1676116 5.6642827 9.8496995 - 6700 5.423067 5.4226985 10.171776 - 6750 4.9274053 5.3926204 9.8502911 - 6800 4.9887802 5.0472917 10.111779 - 6850 4.7201661 4.83946 9.6275293 - 6900 4.6270723 4.3137963 9.9911883 - 6950 4.7942567 4.8427671 9.6135269 - 7000 5.0437851 5.1894655 9.8059441 - 7050 5.4225853 5.6730348 10.380611 - 7100 5.3526725 5.366095 10.809916 - 7150 5.4601926 5.288364 10.565143 - 7200 5.1693092 5.2974578 9.849408 - 7250 4.636056 4.9049993 8.886325 - 7300 4.3959701 4.329844 9.2339636 - 7350 4.565932 4.5362817 9.4502211 - 7400 4.8815031 5.2467956 9.533884 - 7450 5.0423354 5.4958195 10.746164 - 7500 5.4986547 5.4120911 10.642538 - 7550 4.8194458 4.6515196 9.3519793 - 7600 4.3485953 4.9262925 9.2856337 - 7650 4.6044397 4.8926749 9.1169078 - 7700 4.887369 5.14193 10.058145 - 7750 5.5487873 5.5141636 11.432779 - 7800 5.4104699 5.5487467 11.192853 - 7850 4.854184 5.057851 9.6193733 - 7900 4.6510371 4.6445148 9.5905654 - 7950 4.9814759 4.7704719 9.4965789 - 8000 4.7758292 5.1937876 9.4849264 - 8050 4.7782452 4.5663494 9.7289633 - 8100 4.8225098 5.3648384 9.5979339 - 8150 6.0148826 5.3649476 11.154587 - 8200 5.827507 5.5169147 10.572628 - 8250 5.0297257 5.1234338 9.3020411 - 8300 4.6046603 4.5570973 8.8827391 - 8350 5.3644712 5.1981202 10.229824 - 8400 5.1883813 5.4376828 9.9731365 - 8450 5.3046097 5.7491798 11.164114 - 8500 5.2650074 5.1202378 10.749497 - 8550 4.7905964 5.2786974 10.550609 - 8600 4.617429 4.7393959 9.0461214 - 8650 4.6256633 4.5693007 9.3443004 - 8700 4.7009411 4.030803 8.9360375 - 8750 5.3789708 4.760461 9.8339628 - 8800 5.7463414 5.4243514 10.470581 - 8850 5.157278 5.5842305 11.486137 - 8900 5.0475937 5.1205189 10.086114 - 8950 4.5184928 4.7852537 9.5368998 - 9000 4.5055459 4.9449201 9.4658539 - 9050 5.0035206 4.9128749 9.0698534 - 9100 4.821598 4.8336838 9.3036301 - 9150 5.4258294 5.6834484 10.695099 - 9200 6.3446945 5.3907995 11.225169 - 9250 4.8853033 5.4945962 9.8970725 - 9300 4.6751599 4.9974483 9.754605 - 9350 4.8758504 4.905638 9.4632169 - 9400 4.7936798 4.9838949 10.272661 - 9450 5.0815525 5.4520368 9.6176533 - 9500 5.6312632 5.5596893 10.352406 - 9550 5.0373182 5.0675577 10.549761 - 9600 4.9424044 4.7441107 9.6055995 - 9650 4.4176445 4.6896883 8.9482316 - 9700 4.8480419 4.9664903 10.140515 - 9750 5.0869492 5.6569476 10.616019 - 9800 5.6557237 5.4549563 10.34766 - 9850 5.4099086 5.6741059 10.187811 - 9900 4.8200517 4.931253 9.0858362 - 9950 4.6887887 4.9860091 10.703951 - 10000 5.266225 5.2694816 9.5314566 -Loop time of 2.5963 on 4 procs for 10000 steps with 500 atoms + 50 8.656807 7.9950197 15.884241 + 100 11.492654 12.329741 17.658703 + 150 8.6981119 8.6206624 14.114117 + 200 6.1456927 6.4457399 11.199275 + 250 5.5832485 5.5648091 10.400142 + 300 6.1328799 6.3010248 12.010437 + 350 7.1731722 7.5434426 14.588724 + 400 9.3347098 8.6490053 16.710495 + 450 9.5796766 8.9745197 18.230488 + 500 8.4810279 7.6334377 15.050771 + 550 6.5621497 7.401369 12.711355 + 600 6.5868791 6.4912059 13.361745 + 650 7.8188208 7.1180707 14.27939 + 700 7.6714427 7.8664221 14.845323 + 750 7.1545214 8.1596642 14.255973 + 800 8.1950867 8.6441653 15.642584 + 850 8.5624856 8.4004153 15.303218 + 900 7.2513726 7.522694 12.951416 + 950 6.9147537 7.4166804 13.712135 + 1000 7.9356647 7.9447497 14.787788 + 1050 8.0049909 8.3262071 15.736553 + 1100 7.47785 7.8850623 15.063921 + 1150 7.5982542 7.3264305 14.300792 + 1200 7.7141298 7.2955704 14.347839 + 1250 7.421808 7.0057566 13.701565 + 1300 8.0349263 7.8960785 14.360692 + 1350 7.6034411 8.1859894 15.296327 + 1400 7.7403226 7.7959668 15.155558 + 1450 8.0224022 7.2883482 14.979638 + 1500 7.4472686 7.4123823 14.065575 + 1550 7.8838674 7.3268327 14.0089 + 1600 7.7051065 7.6970609 15.025602 + 1650 8.3761114 7.8808173 16.143239 + 1700 7.8493638 7.9974325 15.369229 + 1750 6.7616091 6.9586731 13.253666 + 1800 6.7881829 6.4387333 13.293849 + 1850 7.4819924 8.113677 15.259022 + 1900 7.7619407 7.345373 14.252099 + 1950 9.1160797 8.6024027 16.442885 + 2000 8.8133522 8.1946233 15.676227 + 2050 7.9252468 7.5817269 14.615024 + 2100 7.3824657 7.2766684 15.063532 + 2150 6.8894956 6.7372708 13.607409 + 2200 7.039392 6.685916 13.545476 + 2250 8.0218429 7.5526941 15.263216 + 2300 8.0069299 7.9230893 16.349675 + 2350 7.8564415 8.2913478 14.62257 + 2400 7.4027437 7.0289244 14.244477 + 2450 8.1596868 6.9974968 13.956696 + 2500 7.3792516 6.7751363 13.897864 + 2550 8.7661201 7.9457114 15.3879 + 2600 8.3077502 7.4606043 15.518229 + 2650 7.5270266 8.1888278 14.833414 + 2700 7.9433204 7.872351 15.415577 + 2750 6.9284646 7.2785928 14.175083 + 2800 7.5239578 7.4370418 13.774583 + 2850 6.8456524 7.1993417 13.82663 + 2900 7.9547454 7.8797239 14.967569 + 2950 8.1366854 7.989168 15.722064 + 3000 7.7915591 7.7902194 14.887574 + 3050 8.3076915 8.5022034 15.966604 + 3100 7.3679745 7.2951683 15.032507 + 3150 6.3983597 7.1922179 14.248095 + 3200 7.3135998 7.6677326 14.588216 + 3250 7.7051677 7.4126323 13.935215 + 3300 7.8377055 7.7808126 15.481713 + 3350 8.4304815 8.5666028 14.52102 + 3400 8.090996 7.722647 15.150921 + 3450 8.3389456 7.5739975 14.33015 + 3500 7.6623037 7.2930598 14.361376 + 3550 7.6117545 6.9106485 13.851755 + 3600 7.1508283 7.6269826 13.535534 + 3650 7.4910852 7.9176295 15.691413 + 3700 8.4802801 8.6324769 16.762136 + 3750 7.022402 7.3282804 14.110888 + 3800 7.5627539 7.0503911 14.55662 + 3850 7.2787215 7.2608067 15.046768 + 3900 7.5355799 6.4532442 14.167082 + 3950 8.048962 7.8525579 15.059109 + 4000 7.3175513 8.1005178 14.269317 + 4050 7.520408 8.2682863 14.522748 + 4100 7.6146474 7.7910616 15.199754 + 4150 7.3099191 7.3588162 14.685704 + 4200 7.7659083 7.2886996 14.33525 + 4250 7.5326919 7.4415236 13.874457 + 4300 7.6950275 8.0507821 14.302796 + 4350 7.7170173 8.8246914 14.911061 + 4400 8.0055097 8.4924898 16.225929 + 4450 7.4405645 8.6425584 14.0991 + 4500 6.4050093 6.813939 13.138703 + 4550 6.47962 7.1644972 14.236311 + 4600 7.8672141 7.2404922 15.653959 + 4650 8.1942529 7.4061361 14.232369 + 4700 7.8827633 7.9150952 15.400505 + 4750 7.5095565 7.5093531 15.016387 + 4800 7.75753 7.5830004 14.189254 + 4850 7.840715 7.4954187 15.121937 + 4900 7.5058956 7.5009855 13.389342 + 4950 7.9778116 7.5810052 14.869835 + 5000 8.0941013 7.5222021 15.321999 + 5050 8.6041139 8.3498159 16.208856 + 5100 7.8357702 7.8500124 14.954782 + 5150 8.1036917 7.5357815 15.714879 + 5200 7.4868525 7.4885485 14.167469 + 5250 6.9392666 6.3711563 13.014779 + 5300 7.7294001 7.5681854 14.60363 + 5350 8.2947591 7.5597033 15.076707 + 5400 7.8365134 8.3559985 14.451289 + 5450 7.6577176 7.8573581 14.649332 + 5500 7.6344288 7.6731281 14.411212 + 5550 7.2854884 7.2377463 14.580478 + 5600 7.6332558 7.5037409 14.809068 + 5650 7.2491454 7.5479013 15.196638 + 5700 7.5027918 8.0434388 14.006705 + 5750 8.4679702 7.2893309 15.600406 + 5800 8.11675 8.7790839 15.150116 + 5850 7.8571033 7.1044939 14.730559 + 5900 7.4555155 6.8841813 13.743156 + 5950 7.4269873 7.4363562 13.722307 + 6000 7.014144 7.2841802 14.010536 + 6050 8.2802859 8.741796 16.724881 + 6100 7.9607544 8.2594316 14.965005 + 6150 7.7505098 7.6437264 14.941281 + 6200 7.2637841 7.2845655 14.922083 + 6250 7.4781943 7.3184749 14.627774 + 6300 7.0053246 7.6973025 14.77968 + 6350 6.9682271 7.2193417 13.261589 + 6400 7.6344736 7.5178683 15.586197 + 6450 8.1803746 8.9186636 15.298001 + 6500 7.9535931 8.0466048 15.058292 + 6550 8.056327 8.7108507 15.645091 + 6600 7.3980755 7.087917 13.188502 + 6650 7.3835052 7.2608077 13.95146 + 6700 7.65293 7.0795957 13.742847 + 6750 7.3562754 7.9842502 14.9349 + 6800 8.2494698 8.1508069 15.314676 + 6850 8.1303284 7.8202726 14.50709 + 6900 6.8743362 7.177725 13.485731 + 6950 7.9101459 7.9096716 14.503653 + 7000 7.8164436 8.3236187 16.081817 + 7050 7.7467975 8.7347369 14.9306 + 7100 7.7324222 7.1489428 14.130705 + 7150 6.7791769 6.9011542 14.121399 + 7200 7.6561999 7.5106057 15.234413 + 7250 8.1336506 8.2347678 15.24865 + 7300 6.9098706 7.1934869 14.762268 + 7350 7.1656572 7.7495163 13.867435 + 7400 7.4777956 7.0012888 14.888226 + 7450 8.3176523 7.7845549 15.400925 + 7500 8.2660801 7.5249967 15.313452 + 7550 7.8682936 7.2724016 15.760637 + 7600 7.3975227 7.5654528 13.588662 + 7650 6.7264804 7.1183131 13.219998 + 7700 7.5072355 7.5540796 15.22008 + 7750 7.7421897 8.0113389 14.385238 + 7800 7.6120438 7.9292888 14.66559 + 7850 8.1731646 7.7092319 15.005626 + 7900 8.2285993 8.0637538 15.54714 + 7950 7.7466424 8.3179588 15.10088 + 8000 6.9988726 7.2092201 12.502859 + 8050 7.0919479 7.0585849 14.613424 + 8100 8.0428791 7.8888417 15.945665 + 8150 8.5677024 8.6618742 15.592526 + 8200 7.5972541 7.6902215 14.030522 + 8250 6.8185307 7.1945156 14.452569 + 8300 7.6384046 7.9698235 13.64607 + 8350 7.8378987 7.547662 15.437631 + 8400 8.2496937 7.8279926 14.684647 + 8450 7.5583846 7.5449624 13.393606 + 8500 7.9690263 7.4398188 15.172533 + 8550 8.9148619 8.1181912 14.965998 + 8600 7.9055582 7.8323691 14.778383 + 8650 7.846331 7.3302071 13.812249 + 8700 7.2669615 6.9949093 14.232954 + 8750 7.7494364 7.4431371 13.748379 + 8800 7.9660017 7.6941365 14.366261 + 8850 7.6599154 7.8343017 14.753737 + 8900 7.623307 7.5207726 15.324822 + 8950 7.4784899 7.7901163 15.290832 + 9000 7.93144 8.1349231 16.08637 + 9050 7.7550193 7.6966669 14.554758 + 9100 7.7952657 7.6029648 13.828782 + 9150 7.2915866 7.2140714 13.882209 + 9200 6.8619177 7.2210075 13.702975 + 9250 8.0756482 7.5893593 15.954582 + 9300 8.022774 7.5747016 14.507683 + 9350 7.4993526 8.1111805 14.917379 + 9400 8.8254745 8.0723829 15.717736 + 9450 7.1983725 7.6626286 13.97487 + 9500 7.0602895 7.6733732 13.883137 + 9550 6.5519083 7.4242978 13.607039 + 9600 8.4732891 7.4177194 15.533846 + 9650 8.9193417 8.5982503 16.110043 + 9700 7.8935173 7.8222315 14.42615 + 9750 7.2393047 7.545224 14.557362 + 9800 6.8495209 7.0841522 13.812737 + 9850 6.9791315 7.5743519 13.013286 + 9900 7.4984681 7.8699746 14.977208 + 9950 8.2030761 8.9314031 17.23834 + 10000 9.3670418 8.2034985 15.902349 +Loop time of 1.5138 on 4 procs for 10000 steps with 500 atoms -Performance: 1663904.185 tau/day, 3851.630 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 2853736.392 tau/day, 6605.871 timesteps/s +98.4% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.28841 | 0.29049 | 0.29324 | 0.3 | 11.19 -Neigh | 1.0622 | 1.078 | 1.0899 | 1.0 | 41.52 -Comm | 0.55877 | 0.56907 | 0.58702 | 1.4 | 21.92 -Output | 0.0028131 | 0.0034448 | 0.0052423 | 1.8 | 0.13 -Modify | 0.54339 | 0.54747 | 0.54917 | 0.3 | 21.09 -Other | | 0.1078 | | | 4.15 +Pair | 0.16778 | 0.17518 | 0.17885 | 1.0 | 11.57 +Neigh | 0.55898 | 0.57272 | 0.59026 | 1.6 | 37.83 +Comm | 0.31971 | 0.33993 | 0.36759 | 3.1 | 22.46 +Output | 0.003036 | 0.0033901 | 0.0042133 | 0.8 | 0.22 +Modify | 0.34512 | 0.35303 | 0.35965 | 0.9 | 23.32 +Other | | 0.06956 | | | 4.60 -Nlocal: 125 ave 128 max 121 min -Histogram: 1 0 0 0 0 1 0 1 0 1 -Nghost: 453.75 ave 460 max 450 min -Histogram: 1 0 1 1 0 0 0 0 0 1 -Neighs: 845 ave 874 max 787 min -Histogram: 1 0 0 0 0 0 0 1 1 1 +Nlocal: 125 ave 132 max 121 min +Histogram: 2 0 0 0 1 0 0 0 0 1 +Nghost: 478 ave 488 max 470 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Neighs: 915.25 ave 981 max 889 min +Histogram: 3 0 0 0 0 0 0 0 0 1 -Total # of neighbors = 3380 -Ave neighs/atom = 6.76 -Neighbor list builds = 4592 +Total # of neighbors = 3661 +Ave neighs/atom = 7.322 +Neighbor list builds = 4485 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:02 +Total wall time: 0:00:01 diff --git a/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.1 b/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.1 index 726ef62179..2c13448192 100644 --- a/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.1 +++ b/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.1 @@ -1,2 +1,281 @@ LAMMPS (22 Sep 2017) -Total wall time: 0:00:02 +# uniaxial NVT deformation of WCA fluid + +units lj +atom_style atomic + + +pair_style lj/cut 1.122562 +read_data data.wca + orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities +pair_coeff 1 1 1.0 1.0 +pair_modify shift yes + +neighbor 0.5 bin +neigh_modify delay 0 + +change_box all triclinic + triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) + +fix 1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5 + +fix 2 all momentum 100 linear 1 1 1 + +#dump 1 all atom 25 dump.lammpstrj + +#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs + +thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] + +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.62256 + ghost atom cutoff = 1.62256 + binsize = 0.811281, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.742 | 2.742 | 2.742 Mbytes +Step c_1_press[1] c_1_press[2] c_1_press[3] + 0 6.3937851 7.0436438 6.4461087 + 50 10.369902 10.999889 6.5437384 + 100 12.411384 13.145871 7.8892802 + 150 12.88182 12.114068 7.5155182 + 200 10.375571 10.979773 6.5624056 + 250 10.158901 10.251273 5.4525068 + 300 10.011314 9.8371382 5.4031393 + 350 9.4890008 9.7992108 5.054963 + 400 9.1715116 9.2647886 4.9600208 + 450 9.8495961 9.3353483 4.986786 + 500 9.5903809 8.576173 4.8252116 + 550 8.8057509 9.7152078 4.9089022 + 600 8.9743682 10.031277 4.8924072 + 650 10.233852 9.3059527 5.1977058 + 700 9.2361906 9.6439971 5.0923763 + 750 10.449751 9.5911465 5.2548714 + 800 9.8366857 9.9873885 4.9456956 + 850 10.266351 9.9620134 5.0602713 + 900 9.6325813 9.3910946 5.1466624 + 950 9.1911919 9.1519006 4.8275345 + 1000 9.2871712 9.8508501 5.2674099 + 1050 9.7052035 10.291793 5.160359 + 1100 9.9425552 10.361827 5.5520484 + 1150 10.377563 10.26588 5.5997436 + 1200 9.6368269 10.354413 5.4137873 + 1250 9.2071055 9.1706334 4.9800411 + 1300 9.7140516 8.7257777 4.8536943 + 1350 10.145983 9.8247797 4.8921813 + 1400 9.1998975 9.6935675 5.2269871 + 1450 9.4838136 8.9035726 4.6867121 + 1500 9.066389 9.811658 4.8875316 + 1550 10.007083 9.8946118 5.204609 + 1600 9.722137 9.9291588 5.326712 + 1650 9.7424614 9.6995966 5.3577819 + 1700 9.7185135 9.5922931 5.385856 + 1750 9.6368481 8.1414594 5.0046079 + 1800 9.8065782 9.6798036 4.92473 + 1850 9.0463737 10.024205 5.6495695 + 1900 9.0774484 10.527582 5.0363426 + 1950 9.1691461 10.049703 4.8517514 + 2000 9.7619602 10.049532 5.2088038 + 2050 9.9203348 9.8056395 5.7699852 + 2100 9.1455665 9.5864018 5.1410542 + 2150 8.8501135 9.7917307 5.141824 + 2200 9.1433685 9.8168548 5.1742441 + 2250 9.3248968 10.454532 5.5456356 + 2300 10.210505 9.361499 5.0935226 + 2350 9.5041186 9.598986 5.2451005 + 2400 8.968896 9.2811921 4.7799868 + 2450 9.8201159 10.133892 4.9981817 + 2500 9.4421084 9.7875766 5.4124809 + 2550 9.6410643 9.9148309 5.0603288 + 2600 9.3810676 9.5346849 5.3233836 + 2650 9.2340337 8.7233538 5.0361302 + 2700 9.405597 9.7848488 4.7537042 + 2750 9.9447412 9.2366502 4.9736459 + 2800 10.189443 9.452684 5.624362 + 2850 9.6680124 9.0941543 5.0101469 + 2900 8.4350889 9.1595018 4.7706866 + 2950 9.0056117 9.3498593 4.7655963 + 3000 9.4795416 9.7400747 5.4705868 + 3050 9.6605264 9.4558374 5.1240166 + 3100 9.681451 9.7966554 5.3174458 + 3150 9.7887528 9.7371194 4.9349103 + 3200 9.9720054 9.5592538 5.2306417 + 3250 10.185023 9.9436037 5.4127312 + 3300 9.9670676 9.6069307 5.026261 + 3350 9.0090411 9.5975249 4.8881019 + 3400 9.6535707 9.748683 4.9933873 + 3450 9.7774977 9.7570511 4.8512619 + 3500 9.7250053 10.36386 5.4057249 + 3550 9.567788 9.773413 5.3936671 + 3600 9.2094148 9.0211247 5.2328675 + 3650 9.3512098 9.73407 4.576624 + 3700 9.159074 9.2611591 5.2996448 + 3750 9.4772798 8.9792211 5.1007079 + 3800 9.3898357 9.1150609 5.2126508 + 3850 9.2466312 9.1460651 4.867472 + 3900 9.9316993 9.3061137 5.1219265 + 3950 9.2550913 9.780254 5.371885 + 4000 10.005356 9.7328972 5.2535791 + 4050 9.5228242 9.5134113 5.4181393 + 4100 9.576808 10.082425 5.1272491 + 4150 10.20265 9.6667058 5.529118 + 4200 9.9443671 10.09427 5.6163734 + 4250 9.4956875 9.9462818 5.0820085 + 4300 10.350144 10.003702 5.1621505 + 4350 10.119486 9.8691507 5.4913457 + 4400 9.4991604 10.516185 5.2512264 + 4450 9.0812854 9.2835603 5.1695714 + 4500 9.7538478 8.5298834 4.5954607 + 4550 9.8920394 9.3581299 5.202587 + 4600 9.2694921 9.3338291 5.201958 + 4650 10.925818 9.5062049 4.8694531 + 4700 11.020014 10.130224 5.582409 + 4750 9.5005142 9.3571561 5.456739 + 4800 9.6670147 9.6628702 5.0451252 + 4850 9.134147 9.1308788 4.7950594 + 4900 9.7466206 8.6171443 4.8716275 + 4950 9.0397505 9.1996036 5.2010502 + 5000 9.6898652 9.8914655 5.3959279 + 5050 10.06771 9.7523891 5.3690408 + 5100 10.000963 9.6279379 5.4077384 + 5150 9.8686159 10.179702 5.0686824 + 5200 9.8866247 9.725152 5.4350049 + 5250 9.2068346 10.214424 5.3187713 + 5300 9.713992 9.8069045 5.496359 + 5350 9.423852 9.364085 5.2144606 + 5400 9.4350241 9.5584633 5.0339001 + 5450 10.555124 10.784922 5.1938072 + 5500 9.4147344 10.33187 5.4360602 + 5550 9.8514653 9.6575827 5.4959779 + 5600 9.3138107 9.6592624 4.941387 + 5650 9.1224809 8.7112257 5.0435936 + 5700 8.8289158 10.749686 4.8916132 + 5750 9.7200279 10.030606 5.2033161 + 5800 9.8439873 9.6289015 5.5131934 + 5850 9.6257294 9.4128988 4.9196038 + 5900 9.7490214 9.5776313 5.0301815 + 5950 9.1430855 10.108944 5.1406243 + 6000 9.3358644 9.5633737 4.9787073 + 6050 9.4432774 8.9464304 5.1466052 + 6100 8.8878373 9.5048946 4.9190238 + 6150 9.6451898 9.2419823 5.0159841 + 6200 9.5042173 8.9414307 5.2634247 + 6250 9.0896505 9.7230651 5.3340322 + 6300 8.8100599 8.8781352 5.4117914 + 6350 9.3104601 9.0233294 5.3136432 + 6400 9.368101 9.6387362 4.7833216 + 6450 10.334343 9.8384149 5.3606204 + 6500 9.8824036 10.022627 6.0857086 + 6550 9.7034443 10.026765 5.17604 + 6600 9.3757845 9.899268 5.2301359 + 6650 10.540821 10.4343 5.5287065 + 6700 9.6317649 9.8923579 5.6045768 + 6750 9.5982772 10.07897 5.1221451 + 6800 10.239883 10.189967 5.3167447 + 6850 10.017271 9.7680902 5.229621 + 6900 9.6200416 10.129301 5.1998759 + 6950 9.0361417 8.923798 5.1652612 + 7000 9.3153521 9.063054 4.6860773 + 7050 8.6434091 9.0363436 4.7811975 + 7100 9.4955395 9.3830541 5.022538 + 7150 9.3392402 9.1847119 5.1544622 + 7200 9.4676321 9.8370036 4.8854442 + 7250 9.5115882 10.350324 4.9780525 + 7300 9.6025583 9.6247917 5.473794 + 7350 9.8919524 10.049446 4.9816931 + 7400 9.6814319 9.9410894 5.265078 + 7450 9.4130955 10.191436 5.2531256 + 7500 9.8114668 8.8461635 5.0562894 + 7550 10.321567 9.4730124 5.2043655 + 7600 9.5059024 9.8330367 5.0749721 + 7650 10.067084 10.606423 5.5598818 + 7700 10.896159 10.084281 5.5159718 + 7750 9.754306 10.162301 5.2475876 + 7800 9.7278145 9.801009 5.0685504 + 7850 9.8639905 10.323104 5.2458864 + 7900 9.7246799 9.1377357 5.1841319 + 7950 10.381792 9.6977533 5.0977386 + 8000 9.7265224 9.2999829 4.7925571 + 8050 9.5203288 9.3144956 4.7539211 + 8100 9.6900973 9.6614063 5.304712 + 8150 9.713677 9.9154149 4.8178575 + 8200 9.4733597 9.8948632 5.036112 + 8250 9.7783036 9.9554334 5.3355682 + 8300 9.4034783 9.9156801 5.5539279 + 8350 9.2984025 9.2013949 5.0753991 + 8400 9.9299078 9.6166801 5.115776 + 8450 9.526737 9.3312125 4.7800587 + 8500 9.581956 10.065906 4.9756092 + 8550 9.2767953 9.326006 5.3024978 + 8600 9.799968 8.4660845 5.0199109 + 8650 9.8985354 10.127852 4.9098064 + 8700 8.7952691 10.521133 5.6840528 + 8750 9.8299997 9.5588553 5.3085734 + 8800 9.0811776 9.5704532 5.1684993 + 8850 9.8303571 9.7618932 5.1251259 + 8900 9.9238794 9.9654863 5.2999683 + 8950 10.851304 9.9682289 5.4133763 + 9000 9.5523794 9.1890766 5.1469144 + 9050 9.7461948 8.9611236 4.9490826 + 9100 10.138917 9.6757567 5.0473544 + 9150 9.4869835 9.4786575 5.0142464 + 9200 10.263518 10.079135 5.1493398 + 9250 9.8691684 9.0908275 5.3221203 + 9300 9.8586707 9.4177643 5.1525265 + 9350 9.3375816 9.9167208 5.4846207 + 9400 9.5603903 9.4813199 4.6237495 + 9450 10.30892 9.5217736 5.6163214 + 9500 9.327949 9.9831649 4.8923915 + 9550 9.8421656 9.3202702 5.3352046 + 9600 8.8543704 9.4556702 4.6430041 + 9650 10.103399 9.2161072 4.8658062 + 9700 9.507811 9.9647378 5.227369 + 9750 9.4988096 8.9942893 5.2491418 + 9800 9.8007958 9.234452 5.1740203 + 9850 9.6029685 10.076042 5.023107 + 9900 9.4035691 10.13782 5.2775777 + 9950 9.6517135 10.355994 5.3035779 + 10000 9.9157616 9.7741952 5.5269431 +Loop time of 3.47119 on 1 procs for 10000 steps with 500 atoms + +Performance: 1244529.812 tau/day, 2880.856 timesteps/s +99.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.53077 | 0.53077 | 0.53077 | 0.0 | 15.29 +Neigh | 2.219 | 2.219 | 2.219 | 0.0 | 63.93 +Comm | 0.21866 | 0.21866 | 0.21866 | 0.0 | 6.30 +Output | 0.0027909 | 0.0027909 | 0.0027909 | 0.0 | 0.08 +Modify | 0.41956 | 0.41956 | 0.41956 | 0.0 | 12.09 +Other | | 0.08042 | | | 2.32 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 908 ave 908 max 908 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3489 ave 3489 max 3489 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3489 +Ave neighs/atom = 6.978 +Neighbor list builds = 4567 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:03 diff --git a/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.4 b/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.4 index fd366b7711..276eb2f443 100644 --- a/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.4 +++ b/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.4 @@ -67,215 +67,215 @@ Step c_1_press[1] c_1_press[2] c_1_press[3] 800 9.8366858 9.9873885 4.9456956 850 10.266351 9.9620134 5.0602713 900 9.6325811 9.3910947 5.1466627 - 950 9.1911905 9.1518996 4.8275336 - 1000 9.2871726 9.8508563 5.2674079 - 1050 9.7052021 10.291782 5.1603606 - 1100 9.9425831 10.361849 5.5520586 - 1150 10.37757 10.265897 5.5997238 - 1200 9.636703 10.354446 5.4138755 - 1250 9.2075215 9.1705175 4.9806575 - 1300 9.7125393 8.7247632 4.8527793 - 1350 10.146277 9.8323819 4.8958397 - 1400 9.1957181 9.7052513 5.2335098 - 1450 9.4667213 8.9007965 4.7073369 - 1500 9.0965389 9.8398957 4.8891559 - 1550 10.06178 9.8138538 5.1638382 - 1600 10.143509 9.7138732 5.0784492 - 1650 9.9512338 9.8872687 5.1954485 - 1700 9.3001767 8.4717446 4.9066425 - 1750 9.1538623 9.449051 4.9792008 - 1800 10.647126 9.9223864 4.9100709 - 1850 10.58929 9.5949045 5.4586105 - 1900 9.1522315 10.1302 5.1997482 - 1950 9.101169 9.4253005 5.1420221 - 2000 9.6193051 9.6907925 5.1624939 - 2050 9.6709026 9.9097494 5.0839389 - 2100 10.057719 9.4467483 4.8687849 - 2150 9.1739276 9.1641054 5.1634915 - 2200 9.5136146 9.2946745 4.9764961 - 2250 9.3797544 9.1230688 5.0899386 - 2300 10.298029 9.4044845 5.2381589 - 2350 9.9207185 9.7553339 5.1366828 - 2400 9.6642531 9.8963683 4.8646464 - 2450 8.7643842 9.3435464 4.9072249 - 2500 9.5049695 9.5989949 5.0092494 - 2550 9.6320496 9.4008794 4.8200251 - 2600 9.903178 9.4782306 5.0650137 - 2650 9.4189501 9.2165039 5.1789521 - 2700 9.0208832 9.348362 4.8609921 - 2750 9.6783103 9.8040877 5.0079603 - 2800 10.031195 10.619877 5.374209 - 2850 9.8303748 10.254827 5.3671813 - 2900 9.1249173 8.5172277 5.2143577 - 2950 9.0730525 9.2540699 4.8573951 - 3000 9.9958033 9.6279178 5.1505831 - 3050 9.3665306 9.5285363 5.1160245 - 3100 9.299668 9.0685264 5.0511145 - 3150 9.0579805 9.4816527 5.2936574 - 3200 9.5941 9.7325027 5.1824229 - 3250 10.194794 9.4171587 5.443428 - 3300 9.5927373 9.4430409 4.8998086 - 3350 9.9600944 9.4542266 5.5225391 - 3400 9.7209098 10.024835 5.535451 - 3450 8.6519155 8.9415312 4.8385083 - 3500 10.096352 8.8783306 4.9350231 - 3550 9.3491636 9.5548236 5.2751 - 3600 9.6919611 9.7076185 5.1635464 - 3650 10.481089 9.4863551 5.3286659 - 3700 9.5756116 9.2201941 5.226026 - 3750 9.6434932 9.5295221 5.0288715 - 3800 9.9269327 10.205704 4.7808382 - 3850 9.3189899 10.218335 4.83239 - 3900 9.609462 9.3080222 5.0195027 - 3950 9.5231033 8.869665 5.1015894 - 4000 9.6412436 9.3303396 4.8401661 - 4050 9.8174742 9.4591309 5.4392126 - 4100 9.7799256 9.6304628 4.672532 - 4150 9.8013021 10.139168 5.5527338 - 4200 9.2342593 9.2257279 5.2050637 - 4250 10.018762 10.415623 5.389449 - 4300 9.0369099 8.3453432 4.8345057 - 4350 9.6482435 9.2127862 4.7007287 - 4400 9.1131695 8.4018843 5.1782917 - 4450 9.1035579 9.6671216 4.8282646 - 4500 8.9284156 9.8070543 4.8713415 - 4550 10.131312 9.8932255 4.9533532 - 4600 10.077058 10.137857 5.0295905 - 4650 10.173958 9.1894558 5.6784615 - 4700 9.4202409 8.6802878 5.0213632 - 4750 9.9258459 9.3402009 5.3392346 - 4800 9.8529686 9.5514806 5.1122451 - 4850 10.161646 9.244328 5.1681917 - 4900 9.3419622 9.8193483 5.2391261 - 4950 9.4263728 10.150522 5.043291 - 5000 9.3869223 9.1981116 5.1708012 - 5050 8.9996015 9.4572528 5.1843173 - 5100 8.9894979 9.5093357 4.8005208 - 5150 9.7942953 9.7335166 5.198425 - 5200 9.8904105 9.8505698 5.3255803 - 5250 10.222488 9.0105229 5.0736676 - 5300 9.1670895 10.615218 5.323205 - 5350 9.7642772 9.6199466 5.5903157 - 5400 8.8178616 9.1035263 4.9848621 - 5450 9.6779115 9.5531466 5.0626435 - 5500 9.4723384 9.8744061 4.8594102 - 5550 9.2659141 9.3866112 5.1213249 - 5600 9.9307711 10.011157 4.7073137 - 5650 9.1360772 10.050505 5.3293825 - 5700 8.9098929 9.7579153 5.3489592 - 5750 8.7670629 9.3719349 5.4463723 - 5800 9.0459529 8.7757212 4.8544378 - 5850 9.434501 9.7207864 4.7607373 - 5900 9.1211752 9.7909617 5.4247162 - 5950 10.12889 10.010702 5.360621 - 6000 9.703862 9.3482478 5.0059776 - 6050 9.9038104 8.8812394 5.1991618 - 6100 9.5438555 9.4415027 4.9217198 - 6150 10.192211 9.2429673 5.1715813 - 6200 10.306686 9.1384768 4.7312526 - 6250 9.4873042 9.9164005 5.0562414 - 6300 9.8842909 9.730243 5.1300241 - 6350 9.9418731 9.9679301 5.0582982 - 6400 9.4128222 9.292455 5.4644225 - 6450 8.7305012 8.0605057 4.5415131 - 6500 8.8577233 8.5832574 4.40194 - 6550 9.6163915 9.2509075 5.1138801 - 6600 10.128781 10.078794 5.4904826 - 6650 9.6019333 9.5285605 5.58386 - 6700 10.021737 10.073117 5.1420822 - 6750 10.495681 10.002678 5.0176241 - 6800 9.9675843 10.053135 5.3183498 - 6850 9.2289727 9.2937883 5.2061573 - 6900 9.3004627 9.8324369 4.9496725 - 6950 9.02096 9.3364941 4.9229962 - 7000 9.5391177 9.1122871 5.1137302 - 7050 9.5599 9.5978836 5.1530405 - 7100 9.4939385 9.641504 5.3032985 - 7150 9.7088291 9.7821494 5.0252857 - 7200 9.6044672 8.9831056 4.7110805 - 7250 9.1933876 9.044105 5.1760484 - 7300 8.8666209 8.8262052 5.0675085 - 7350 8.9601722 8.8080504 4.6713412 - 7400 9.7343434 9.230838 5.0227894 - 7450 10.465298 10.086546 5.3538547 - 7500 9.8348497 9.6682345 5.6155581 - 7550 9.2055261 9.9530385 5.2999975 - 7600 10.058087 10.359037 5.5097355 - 7650 10.049127 9.1073265 5.677653 - 7700 9.8658364 9.3018637 5.1476764 - 7750 9.1199366 9.0783067 5.0848865 - 7800 8.8578293 8.7974398 5.2016434 - 7850 9.775635 9.463061 5.3655492 - 7900 9.295538 9.5095055 4.8011116 - 7950 9.6493214 9.8679316 5.5265297 - 8000 9.8347059 9.766271 5.0480481 - 8050 10.221272 9.8343303 5.1569604 - 8100 9.9470574 9.6982535 5.2138091 - 8150 9.7416712 9.9761168 5.3335775 - 8200 9.6885832 9.7871945 5.084485 - 8250 9.4437905 9.6080847 5.1152245 - 8300 9.8251187 9.381407 5.2040497 - 8350 9.997553 10.13024 5.4380783 - 8400 8.964249 9.7006666 5.3283399 - 8450 9.0154607 8.9476167 4.9831421 - 8500 9.7376641 8.943646 4.8864283 - 8550 9.0838444 9.2479888 4.9685049 - 8600 9.6403296 9.8366009 5.0968951 - 8650 9.6635046 10.308254 5.2703839 - 8700 10.365594 10.611924 5.1621352 - 8750 9.805264 10.361514 5.1519855 - 8800 9.5028336 10.227006 5.2248281 - 8850 10.183228 9.921676 5.3720572 - 8900 9.3635214 9.6744843 5.2400037 - 8950 10.670314 9.9503151 5.1614572 - 9000 9.7127361 9.6573131 5.3563693 - 9050 8.7056986 9.0613731 5.046923 - 9100 8.9478272 9.0640872 4.9287586 - 9150 8.8313013 8.5112475 5.2262306 - 9200 9.364301 8.959883 5.0174211 - 9250 10.288615 9.1790518 5.0426516 - 9300 9.617956 9.7241075 5.3777373 - 9350 10.0358 9.5309547 5.4949469 - 9400 9.8158206 10.060424 5.3424158 - 9450 10.005718 9.1139373 4.9685999 - 9500 9.806939 9.6244612 5.1818962 - 9550 10.28972 9.3960873 5.0642479 - 9600 10.312876 9.4252906 5.2704439 - 9650 9.6829433 9.9125054 4.9184741 - 9700 9.6234227 10.008167 5.1544723 - 9750 10.025877 9.4306579 5.3817937 - 9800 9.3702702 9.6149983 4.8804752 - 9850 9.4719715 9.1649874 5.1584215 - 9900 8.9906714 9.1807845 4.8599792 - 9950 9.1661525 9.1219335 4.8148579 - 10000 9.1946626 9.3436899 5.0765307 -Loop time of 2.3144 on 4 procs for 10000 steps with 500 atoms + 950 9.1911906 9.1518996 4.8275336 + 1000 9.2871726 9.8508561 5.2674079 + 1050 9.7052019 10.291782 5.1603609 + 1100 9.9425827 10.361848 5.5520588 + 1150 10.37757 10.265891 5.5997246 + 1200 9.6367069 10.354451 5.4138749 + 1250 9.2075006 9.1705136 4.9806417 + 1300 9.7126123 8.7247301 4.8528533 + 1350 10.146034 9.8319205 4.8958266 + 1400 9.19638 9.7052094 5.2332913 + 1450 9.4667073 8.9014702 4.7073387 + 1500 9.0949401 9.8381729 4.8904182 + 1550 10.068959 9.8096692 5.1613658 + 1600 10.131443 9.7086921 5.0913546 + 1650 9.9557572 9.9183989 5.2635245 + 1700 9.3820418 8.6135867 4.9395498 + 1750 8.9486365 9.3433293 5.2674469 + 1800 10.352322 10.354432 5.3335153 + 1850 8.9629784 9.6172224 5.0824828 + 1900 8.5429652 9.749815 5.1577895 + 1950 8.9828002 8.9631646 5.0948426 + 2000 9.4171989 9.7122117 5.1386251 + 2050 9.767299 9.6146113 4.8965319 + 2100 10.049399 10.02243 5.3856622 + 2150 9.2639644 10.09669 5.3020322 + 2200 9.1916162 10.841127 5.0271109 + 2250 9.9859708 8.519568 5.24568 + 2300 9.9462279 9.5850706 5.0632906 + 2350 9.8043011 9.7605126 5.3148323 + 2400 9.089818 9.6474522 5.0012486 + 2450 9.655874 9.3255636 4.8291262 + 2500 9.0259445 9.3074827 5.1593031 + 2550 9.1610478 9.7356492 5.0741161 + 2600 9.3153881 9.3936949 5.4830363 + 2650 9.6212696 9.598252 4.7172875 + 2700 9.318906 9.665656 5.1917527 + 2750 9.6613838 9.7106796 5.1843146 + 2800 10.231844 9.9407641 4.6940455 + 2850 10.008093 9.2781076 5.2624957 + 2900 10.464168 9.808666 5.1457978 + 2950 9.7080601 9.6972304 5.406456 + 3000 9.6851209 10.050737 5.1198394 + 3050 8.9093581 9.213428 5.233108 + 3100 8.8098921 9.6607476 4.9625331 + 3150 8.6608386 9.7503441 5.0737533 + 3200 9.7004403 9.6748778 5.0734462 + 3250 10.077054 10.318711 5.3233841 + 3300 10.63887 9.4901739 5.516542 + 3350 10.232909 9.3407073 5.4989967 + 3400 9.8854134 9.9542625 5.1982468 + 3450 9.9388203 9.3394716 4.8135833 + 3500 9.2514026 9.5857527 5.4605449 + 3550 8.3940282 9.0549836 4.6951548 + 3600 8.7696659 9.6262816 4.6302087 + 3650 9.0695173 8.8520895 5.0814723 + 3700 9.4700744 9.2777557 4.6825004 + 3750 9.0221844 9.3407486 5.3984156 + 3800 9.1478369 9.1420043 5.3024474 + 3850 9.2652818 9.700053 5.3355364 + 3900 10.248456 9.2480211 5.2375956 + 3950 9.8259922 9.6130415 5.5978761 + 4000 9.404877 9.7931698 5.3767927 + 4050 10.131713 9.7047295 5.2964594 + 4100 9.8128638 9.4253237 5.5308166 + 4150 10.25183 9.1333595 5.1957555 + 4200 10.449736 9.295762 4.7863033 + 4250 9.7304858 9.4482515 5.356439 + 4300 9.2773777 9.4110855 4.9879246 + 4350 8.9325082 9.3429549 5.0410132 + 4400 9.2603855 9.7905381 4.7436126 + 4450 8.7600443 9.9160722 5.196316 + 4500 9.0824514 10.036035 4.873051 + 4550 9.3884333 9.6644343 5.1154951 + 4600 9.8181676 9.6385118 5.3639835 + 4650 9.1574799 9.5386974 4.7487094 + 4700 10.275911 9.5383553 5.1084297 + 4750 9.2476854 9.3353591 5.4773008 + 4800 9.3422407 9.1931821 4.9210291 + 4850 9.9033126 9.6443642 5.1334553 + 4900 9.8469467 9.6836455 5.5101146 + 4950 10.211229 9.760253 5.0151668 + 5000 9.3256273 10.109873 5.4129479 + 5050 9.9704879 9.8504809 5.2191163 + 5100 9.4820718 9.711504 4.9633504 + 5150 9.2952171 9.6955742 5.3214246 + 5200 9.8400791 9.4763906 4.9149518 + 5250 10.080112 9.5634741 5.1701348 + 5300 9.4221014 9.8149742 5.3605931 + 5350 8.8228402 10.121343 5.3192212 + 5400 9.7318719 10.508763 5.0044083 + 5450 8.7429847 9.6583774 5.033313 + 5500 9.9243256 10.239521 5.2956506 + 5550 9.6088558 9.8555986 5.359257 + 5600 10.904352 10.72033 5.7874034 + 5650 9.4774477 9.7246962 5.596949 + 5700 9.8527139 9.2188245 4.6518586 + 5750 9.7932375 9.2763721 4.6663307 + 5800 9.5630073 9.1704583 5.4784197 + 5850 10.159996 9.5206168 5.0012706 + 5900 9.1667978 9.6891715 5.1959301 + 5950 9.2194131 9.2170699 5.1653264 + 6000 9.5917124 9.2038051 5.1004966 + 6050 9.4141124 9.9166471 5.0535712 + 6100 10.231166 9.7746591 5.2399634 + 6150 9.6054192 9.34446 5.0711646 + 6200 9.9279645 8.9546561 5.4698039 + 6250 9.1581437 8.95439 4.9336111 + 6300 8.9257232 9.0665473 5.188718 + 6350 9.7685695 9.0822789 4.8454457 + 6400 9.5140226 9.5073414 5.3420644 + 6450 9.5379198 9.3316002 5.1940338 + 6500 10.216584 9.8982859 5.2790157 + 6550 10.221286 10.913585 5.4521496 + 6600 10.925166 10.088055 5.2079758 + 6650 10.012501 9.3870455 5.1740433 + 6700 10.176139 9.4869588 5.3783369 + 6750 9.2819415 8.1431975 4.8256476 + 6800 9.790723 9.7932943 5.3602927 + 6850 9.1327199 9.8354267 5.1356642 + 6900 9.240909 9.3854618 5.1767268 + 6950 10.652806 9.4355671 5.1314851 + 7000 9.1676917 10.055501 5.2824651 + 7050 9.6486488 9.1063089 4.9596976 + 7100 9.3733678 9.5875095 5.0882285 + 7150 9.282243 9.354934 4.6752644 + 7200 8.7370777 10.1445 5.0217245 + 7250 9.563419 9.929442 5.1720916 + 7300 9.9128346 9.2426863 5.3595023 + 7350 9.9319949 9.9479477 5.4844629 + 7400 9.4671739 9.2380048 5.3274217 + 7450 9.7531193 9.4075641 4.9426738 + 7500 10.331422 9.4704554 5.3036636 + 7550 8.7724434 9.663179 4.9492563 + 7600 10.222748 9.1674852 4.8135992 + 7650 9.5288583 8.5866929 5.0342955 + 7700 8.8832847 8.8035037 4.6184473 + 7750 9.4847076 9.7969656 5.0035855 + 7800 9.2782486 9.1283641 5.3151299 + 7850 8.962989 8.7729872 5.0374817 + 7900 9.6336556 9.4975426 4.9832641 + 7950 10.125279 10.044247 5.2740873 + 8000 9.9705097 9.6925988 5.2344188 + 8050 9.7836318 9.5794261 4.9174534 + 8100 10.79561 10.04809 5.1604639 + 8150 9.7261726 10.372878 5.3083843 + 8200 10.338569 10.08189 5.6555172 + 8250 9.7833315 9.9834209 5.3790753 + 8300 9.5857944 9.6052323 5.0689289 + 8350 9.6706688 9.6189242 4.7725678 + 8400 10.570423 9.5786093 5.1894242 + 8450 9.6514599 10.168359 5.0733592 + 8500 10.273682 9.9179284 5.4014563 + 8550 9.3120287 10.146837 4.9895115 + 8600 9.511943 9.644112 5.462624 + 8650 10.380674 9.1117114 5.156727 + 8700 10.068596 8.7687113 5.1440814 + 8750 9.2484971 9.2477678 4.9318794 + 8800 9.7298469 8.9480303 5.1151321 + 8850 9.7299502 10.415138 4.7902908 + 8900 10.966912 10.732962 5.4793574 + 8950 10.328384 9.9501313 5.6238396 + 9000 9.7385041 9.8319224 5.1926497 + 9050 9.7971055 9.5740203 5.1111302 + 9100 9.7789727 9.9281901 5.1786549 + 9150 9.9306964 9.3360599 4.9524547 + 9200 9.8798841 10.240752 5.1691344 + 9250 10.185445 9.4934917 4.9188964 + 9300 8.9184663 8.9349408 4.8079511 + 9350 9.6552187 9.9846949 4.9619969 + 9400 10.304306 9.2298208 5.2822855 + 9450 9.8379613 10.041703 5.4186514 + 9500 10.221443 9.5342818 4.8929802 + 9550 9.9723047 10.072856 5.4169676 + 9600 9.3923879 9.2984387 5.4452785 + 9650 8.9072589 9.7482374 4.7835208 + 9700 9.8370121 10.205922 5.0385145 + 9750 9.4274542 9.4653248 5.6340681 + 9800 9.7668106 9.3265705 5.3154126 + 9850 10.422549 10.362922 5.361592 + 9900 9.6264407 9.9790162 5.6381052 + 9950 10.35018 9.8853593 5.2639184 + 10000 9.6190853 9.7903758 5.1583115 +Loop time of 1.32471 on 4 procs for 10000 steps with 500 atoms -Performance: 1866574.813 tau/day, 4320.775 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3261084.476 tau/day, 7548.807 timesteps/s +98.4% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.24989 | 0.25356 | 0.25618 | 0.5 | 10.96 -Neigh | 1.0785 | 1.0971 | 1.1047 | 1.0 | 47.40 -Comm | 0.56674 | 0.57565 | 0.59467 | 1.5 | 24.87 -Output | 0.0038562 | 0.0045416 | 0.006454 | 1.6 | 0.20 -Modify | 0.26644 | 0.2701 | 0.27307 | 0.5 | 11.67 -Other | | 0.1134 | | | 4.90 +Pair | 0.1301 | 0.13489 | 0.13886 | 0.9 | 10.18 +Neigh | 0.5654 | 0.575 | 0.5883 | 1.3 | 43.41 +Comm | 0.35135 | 0.37147 | 0.38856 | 2.4 | 28.04 +Output | 0.0028336 | 0.0032777 | 0.004292 | 1.0 | 0.25 +Modify | 0.16328 | 0.16711 | 0.17231 | 0.8 | 12.61 +Other | | 0.07297 | | | 5.51 -Nlocal: 125 ave 135 max 121 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 462.75 ave 468 max 457 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Neighs: 861.75 ave 946 max 830 min -Histogram: 3 0 0 0 0 0 0 0 0 1 +Nlocal: 125 ave 128 max 122 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 477 ave 489 max 469 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Neighs: 861 ave 877 max 848 min +Histogram: 1 0 1 0 0 1 0 0 0 1 -Total # of neighbors = 3447 -Ave neighs/atom = 6.894 -Neighbor list builds = 4556 +Total # of neighbors = 3444 +Ave neighs/atom = 6.888 +Neighbor list builds = 4560 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:02 +Total wall time: 0:00:01 From 588b2534c9b06b9ecc9f2ceb8fe7969949b4d7ce Mon Sep 17 00:00:00 2001 From: David Nicholson Date: Mon, 2 Oct 2017 23:26:21 -0400 Subject: [PATCH 16/21] Minor fix for FixNHUef constructor --- src/USER-UEF/fix_nh_uef.cpp | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp index e2217daa82..dd639c34db 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -112,9 +112,12 @@ FixNHUef::FixNHUef(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Illegal fix nvt/npt/uef command"); iarg += 2; + } else { + + // skip to next argument; argument check for unknown keywords is done in FixNH + + ++iarg; } - // skip to next argument; argument check for unknown keywords is done in FixNH - ++iarg; } if (!erate_flag) From 1dffb0cf82ad25b9ec67bece8c01db457b72b519 Mon Sep 17 00:00:00 2001 From: David Nicholson Date: Mon, 2 Oct 2017 23:27:10 -0400 Subject: [PATCH 17/21] reran npt_biaxial examples --- .../npt_biaxial/log.22Sep17.npt_biaxial.g++.1 | 430 ++++++++--------- .../npt_biaxial/log.22Sep17.npt_biaxial.g++.4 | 438 +++++++++--------- 2 files changed, 434 insertions(+), 434 deletions(-) diff --git a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1 b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1 index 7ef4482b9d..e6d3b30cdb 100644 --- a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1 +++ b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1 @@ -52,233 +52,233 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 2.742 | 2.742 | 2.742 Mbytes Step c_1_press[1] c_1_press[2] c_1_press[3] 0 6.3937851 7.0436438 6.4461087 - 50 8.656807 7.9950197 15.884241 - 100 11.492654 12.329741 17.658703 - 150 8.6981119 8.6206624 14.114117 - 200 6.1456927 6.4457399 11.199275 - 250 5.5832485 5.5648091 10.400142 - 300 6.1328799 6.3010248 12.010437 - 350 7.1731722 7.5434426 14.588724 - 400 9.3347098 8.6490053 16.710495 - 450 9.5796766 8.9745197 18.230488 - 500 8.4810279 7.6334377 15.050771 - 550 6.5621497 7.401369 12.711355 - 600 6.5868791 6.4912059 13.361745 - 650 7.8188208 7.1180707 14.27939 - 700 7.6714427 7.8664221 14.845323 - 750 7.1545213 8.1596642 14.255973 - 800 8.1950866 8.6441652 15.642584 - 850 8.5624855 8.4004152 15.303218 - 900 7.2513729 7.5226938 12.951415 - 950 6.9147541 7.4166796 13.712136 - 1000 7.9356665 7.9447497 14.787789 - 1050 8.0049947 8.3262124 15.736553 - 1100 7.4778576 7.8850531 15.063925 - 1150 7.5982598 7.3264091 14.300757 - 1200 7.7140371 7.2955688 14.347757 - 1250 7.4219774 7.0057022 13.701556 - 1300 8.0349765 7.8954305 14.361289 - 1350 7.6041533 8.1862555 15.296344 - 1400 7.7416819 7.7959914 15.162316 - 1450 8.0188314 7.2866705 14.983598 - 1500 7.4473216 7.3994359 14.067676 - 1550 7.8852675 7.3618461 14.061472 - 1600 7.7365655 7.5982634 14.68822 - 1650 8.3347522 8.1032999 16.189298 - 1700 8.021765 7.6018364 14.337751 - 1750 6.8819319 6.5380502 13.166309 - 1800 6.6099094 6.915077 12.331541 - 1850 7.4163951 7.8158695 14.534615 - 1900 8.4061445 8.3757582 15.887245 - 1950 8.1452338 8.4887365 15.059168 - 2000 8.6938353 9.0101284 16.680096 - 2050 7.4587753 7.7917795 15.211311 - 2100 7.0551172 7.110128 14.141606 - 2150 7.0175122 6.6961241 14.279182 - 2200 6.9961187 7.3322415 13.171629 - 2250 7.5170372 7.2002508 13.655891 - 2300 7.5550073 7.889281 15.268156 - 2350 8.6343715 8.1446746 15.343131 - 2400 7.8734662 8.2266284 15.094857 - 2450 8.4135272 8.7207275 16.025335 - 2500 7.2176413 7.863538 16.295816 - 2550 8.1745427 8.093571 14.982008 - 2600 7.3905296 7.033819 13.473161 - 2650 6.7049957 6.4518564 13.109849 - 2700 7.0979639 7.2722444 13.108017 - 2750 8.013824 7.9399712 14.221876 - 2800 8.4370721 8.6814371 16.44629 - 2850 7.8347153 8.1521156 15.561372 - 2900 8.035115 7.8964336 14.867854 - 2950 7.1672845 7.3532206 15.440881 - 3000 7.5346666 6.9003742 14.27777 - 3050 7.3784203 7.3252438 14.047681 - 3100 7.2587022 6.9154856 13.171992 - 3150 7.2711856 7.7599218 15.241926 - 3200 8.5378786 8.4297377 15.866421 - 3250 8.0342828 8.0687328 15.416609 - 3300 7.5984747 7.2012637 13.601468 - 3350 7.3021124 6.9641186 12.646778 - 3400 7.209707 7.8050641 14.085147 - 3450 7.5112359 7.7338405 15.677763 - 3500 8.8355621 8.8289163 16.331319 - 3550 7.9119042 8.47938 14.393274 - 3600 7.4370847 7.2492674 14.933099 - 3650 7.2371175 7.2652477 13.586608 - 3700 7.172453 6.5367899 14.64114 - 3750 7.3950889 7.1264975 14.372124 - 3800 7.7074509 7.5716747 14.839055 - 3850 7.8509762 8.1926443 15.486783 - 3900 8.0742138 7.8584144 14.887115 - 3950 6.9346973 7.8694823 14.666153 - 4000 7.6621984 7.6382651 14.793905 - 4050 7.4090172 7.3118869 14.993099 - 4100 7.6033087 8.3890976 15.461012 - 4150 8.0450732 8.2172794 16.263521 - 4200 7.1723176 6.8215613 12.761291 - 4250 7.1840793 7.219089 14.163744 - 4300 7.1380776 7.5355394 14.487621 - 4350 7.6523602 7.7530752 15.549788 - 4400 7.9503171 8.0947449 15.058755 - 4450 7.5850837 7.5248838 15.796171 - 4500 7.1597196 7.0346482 13.889614 - 4550 7.5588017 7.4473311 14.513886 - 4600 7.1855439 7.7743654 13.928596 - 4650 7.8936012 8.0911603 15.821516 - 4700 7.5437461 8.4762734 15.249242 - 4750 7.5999136 8.0141389 14.942225 - 4800 7.6708678 7.4003145 13.855277 - 4850 7.5902038 7.0718185 14.676038 - 4900 7.6448398 7.7623026 15.013123 - 4950 8.1761651 8.2132532 15.827257 - 5000 7.5310459 7.9710358 14.570133 - 5050 7.3910867 7.9090596 14.644752 - 5100 7.5096472 8.0032554 14.151557 - 5150 7.4930298 7.6627654 14.776418 - 5200 8.0258893 6.9808848 14.80221 - 5250 7.621093 7.5081066 14.18567 - 5300 7.7724131 7.3547437 13.390993 - 5350 7.7141018 7.4182737 15.383453 - 5400 7.5798525 7.604214 13.772184 - 5450 8.1532137 7.7843706 15.636038 - 5500 8.0049611 7.79693 14.435558 - 5550 8.2449821 7.9493856 15.227616 - 5600 8.3248504 7.6677271 14.929828 - 5650 7.7005024 7.8412131 14.508952 - 5700 7.3062546 7.3272456 13.075895 - 5750 7.2476367 7.1095473 14.729012 - 5800 8.302566 8.358882 14.667741 - 5850 8.3481651 7.7985514 15.305433 - 5900 6.6533193 7.1150305 13.497761 - 5950 7.2385939 7.9132287 14.889887 - 6000 7.5594171 7.7167581 14.878921 - 6050 7.5977124 7.583702 15.842984 - 6100 8.1433134 8.1548274 15.253848 - 6150 7.4371297 7.7036444 13.892215 - 6200 7.3807114 7.2270114 14.32622 - 6250 7.5101996 6.7835902 14.62525 - 6300 7.779059 7.0241215 14.008402 - 6350 7.7217303 7.8795697 14.544095 - 6400 8.0987528 8.2649512 15.615863 - 6450 7.5662457 7.4332335 14.174783 - 6500 7.3672018 7.691987 13.757496 - 6550 7.4424935 7.4401054 14.660643 - 6600 8.0670938 8.4028068 15.558513 - 6650 7.9428662 7.5886468 15.814302 - 6700 7.5792547 7.5877961 14.300332 - 6750 6.6732262 7.5855672 14.322929 - 6800 7.2340735 7.6129085 13.010849 - 6850 7.3530804 7.2093837 14.012405 - 6900 8.1335803 8.1621205 14.290907 - 6950 8.0140455 8.0254163 15.242386 - 7000 7.9944794 8.1150205 15.343835 - 7050 7.6449634 8.4930222 16.254105 - 7100 8.1486038 7.5521474 14.659373 - 7150 6.9146032 7.1979211 13.220697 - 7200 7.1472024 6.8585436 13.747498 - 7250 7.0570799 7.1226848 13.576252 - 7300 7.5713738 7.5064849 14.195069 - 7350 8.6995152 8.4776231 15.983028 - 7400 8.0043956 8.3894875 16.583907 - 7450 7.6606913 7.6695256 13.758723 - 7500 6.925632 7.1358864 13.882849 - 7550 7.284765 7.4400093 12.797499 - 7600 7.1815013 7.0465795 14.661597 - 7650 9.0926556 8.6982979 16.243272 - 7700 9.0289976 8.2542699 15.359908 - 7750 7.6042308 7.350186 15.701097 - 7800 7.7931461 7.5777572 14.397664 - 7850 6.9603382 6.7910235 14.020762 - 7900 7.0994051 6.7555761 13.020541 - 7950 7.4253662 7.0888087 15.177881 - 8000 8.0943311 8.5234668 15.990661 - 8050 7.8770545 8.1329374 14.434819 - 8100 7.114341 7.9621662 15.488984 - 8150 7.6483959 7.7800045 14.790885 - 8200 6.8915301 7.4275666 14.360578 - 8250 6.8943728 7.4597132 13.852787 - 8300 7.5013271 8.0231338 14.983933 - 8350 7.285471 7.5175898 15.318651 - 8400 8.0954536 8.3126472 15.494494 - 8450 7.7122605 7.4228532 15.422058 - 8500 8.0793058 7.077081 14.736069 - 8550 7.1928433 6.8056774 13.691643 - 8600 7.0377566 7.3074361 14.141988 - 8650 7.3824217 7.4739032 14.679069 - 8700 7.7684482 8.1554503 15.191035 - 8750 7.9590885 8.1135479 14.338724 - 8800 8.1231133 7.7860088 15.403904 - 8850 8.5000448 8.1024052 15.173116 - 8900 7.3845853 7.9495964 14.619746 - 8950 7.5818306 7.2248015 14.621207 - 9000 7.2164673 6.6633348 15.609622 - 9050 7.5851603 8.0836264 15.022988 - 9100 7.8771779 7.6350639 14.077462 - 9150 7.6077035 6.8475422 14.315993 - 9200 7.6583735 7.5077759 14.569883 - 9250 7.5263046 7.7028057 14.57854 - 9300 7.2162602 8.053893 16.02041 - 9350 8.3756477 8.1996826 14.70403 - 9400 7.7634122 7.5041574 13.936959 - 9450 7.3067071 7.7438443 14.542518 - 9500 7.4048127 7.44049 14.821218 - 9550 7.2884669 7.9974016 14.367535 - 9600 7.4198667 7.9510424 15.713394 - 9650 7.9099018 8.0161955 15.006711 - 9700 7.3372719 7.419692 14.320242 - 9750 7.2075957 7.3109181 14.541501 - 9800 7.6617849 7.7279899 15.018225 - 9850 7.6595385 7.138483 14.400928 - 9900 7.1440851 7.3065973 12.81291 - 9950 7.5757356 7.3889652 14.59353 - 10000 8.5866601 8.347723 16.125389 -Loop time of 3.74766 on 1 procs for 10000 steps with 500 atoms + 50 7.9020345 7.303289 14.733929 + 100 8.3214325 8.385843 13.166247 + 150 5.7168419 5.6083988 9.7224198 + 200 3.8875348 4.0840705 7.9912973 + 250 4.2933724 4.2410519 7.7200953 + 300 4.5452314 4.2434949 8.6709832 + 350 5.446489 5.6166962 11.300536 + 400 6.0682558 5.7787878 12.106852 + 450 5.3884296 5.5066688 9.9100012 + 500 4.8046418 4.7115986 9.9769201 + 550 4.9043933 4.6240966 9.319336 + 600 4.6843238 4.9571246 9.5325487 + 650 5.1952989 5.195648 9.6187047 + 700 5.4163364 5.2938289 10.136655 + 750 5.6723178 5.0670261 11.415221 + 800 5.9379901 5.6402916 10.815209 + 850 5.0695389 5.3021432 10.742859 + 900 4.6498962 4.7111912 9.8453523 + 950 4.4811641 5.170132 9.421765 + 1000 4.7501483 4.2420772 9.3510803 + 1050 4.5973379 5.2046799 9.8632975 + 1100 4.7879562 4.9051316 9.8658626 + 1150 5.0528771 5.5048545 10.110913 + 1200 4.9926563 5.2482081 9.9610863 + 1250 4.8476232 4.8498859 9.5752989 + 1300 5.2932038 5.0594534 10.869545 + 1350 5.4720421 5.0830442 10.69386 + 1400 4.8175566 4.9863651 10.041898 + 1450 4.6307145 4.5615459 9.231299 + 1500 5.0296259 4.5433558 8.7180513 + 1550 4.8708444 5.1601014 10.256791 + 1600 5.5098593 5.316773 10.224386 + 1650 5.5055907 5.0516814 10.272037 + 1700 4.6965552 5.2436628 9.8272905 + 1750 5.0212307 4.740601 8.9738802 + 1800 4.7756351 5.199734 9.9929449 + 1850 4.7107092 5.177203 10.580427 + 1900 5.0935608 4.5286844 9.3036832 + 1950 4.8035855 4.894359 9.4423987 + 2000 4.5643937 4.7480477 9.4384251 + 2050 4.9314701 4.990414 10.151815 + 2100 5.9828824 5.8188026 12.262691 + 2150 5.5337303 5.4598468 10.136112 + 2200 4.892172 4.8699674 9.1629905 + 2250 4.5680591 4.5740533 9.5633545 + 2300 5.0023535 4.3948659 8.9645774 + 2350 5.2533056 4.9803884 10.255653 + 2400 5.3330196 5.3888322 10.021617 + 2450 5.2095527 4.8765336 10.135381 + 2500 5.221153 5.2974568 10.2493 + 2550 5.385331 5.0801192 10.490479 + 2600 5.3274988 5.0253548 10.147587 + 2650 4.718677 5.2710337 9.7549521 + 2700 4.5811521 4.6083971 8.1923164 + 2750 4.4743752 4.3319737 8.8690805 + 2800 5.0215013 5.2262961 9.8627954 + 2850 6.1005107 5.5994942 11.170661 + 2900 5.9673524 5.362124 10.401699 + 2950 5.5400849 5.7523993 10.292536 + 3000 4.9202636 5.1210431 10.125839 + 3050 4.5286487 5.3586164 9.8634322 + 3100 4.5719961 5.1615414 9.8027972 + 3150 5.4091919 4.8581943 9.96938 + 3200 5.522125 5.3564838 9.7638407 + 3250 4.9019062 5.2514758 9.2993079 + 3300 5.2375918 5.1439012 9.4313575 + 3350 4.750235 4.8692016 10.54193 + 3400 5.5793211 5.4184157 11.021389 + 3450 4.9022614 5.3166498 9.4629659 + 3500 4.6348617 4.4650979 9.0665548 + 3550 4.7922405 4.8961269 10.255446 + 3600 4.8914457 5.1158894 9.4736084 + 3650 5.062771 4.6725475 10.263484 + 3700 5.4842823 5.7793971 10.342915 + 3750 5.3136012 5.063065 10.398307 + 3800 4.9372149 4.9270414 9.5304748 + 3850 5.2144752 5.1716455 9.7575725 + 3900 5.0892665 5.1697057 9.918052 + 3950 5.1124507 5.354702 9.791366 + 4000 5.1255084 5.1143653 10.913101 + 4050 5.1891698 4.9913681 9.6871728 + 4100 4.7663368 4.2435014 8.3815668 + 4150 4.8060033 4.3415868 9.6553386 + 4200 4.8548303 4.8006768 9.5995801 + 4250 5.0976366 5.2683175 10.386444 + 4300 5.8921937 5.5134696 10.788143 + 4350 5.8323871 5.5255869 11.199128 + 4400 5.2464655 5.0005905 10.311055 + 4450 4.9264849 5.2499854 10.26702 + 4500 4.4431895 4.536981 8.7489096 + 4550 4.5180914 4.2080277 8.6525529 + 4600 5.1782188 5.1224059 10.683341 + 4650 5.4156233 4.8714464 10.473939 + 4700 5.3107669 5.224614 10.569391 + 4750 4.9538022 5.2509475 10.288918 + 4800 4.6976945 4.8107142 9.8299772 + 4850 5.1227936 5.0737571 10.440452 + 4900 4.7580514 4.6375995 9.1971008 + 4950 5.0647601 4.6470735 9.583131 + 5000 5.196231 5.7531491 10.409807 + 5050 5.6691323 5.7163652 12.335701 + 5100 5.3603738 5.4887106 10.961712 + 5150 4.455028 4.6494465 9.8096968 + 5200 4.7596912 4.4804896 9.3762885 + 5250 5.3144927 5.0113772 9.553101 + 5300 5.3445266 4.8262035 9.1220802 + 5350 5.1540657 5.5982676 10.765178 + 5400 5.1773418 5.2684381 10.452351 + 5450 4.8946859 5.3283747 9.8015564 + 5500 5.2009608 4.7183522 9.4558009 + 5550 5.4158589 5.5005458 10.539505 + 5600 4.7196831 5.4181991 9.6439249 + 5650 4.8333571 4.8601728 8.9350189 + 5700 5.4395698 4.9730096 10.669681 + 5750 5.2947443 5.6973259 10.020539 + 5800 5.4391993 5.5255143 10.264969 + 5850 4.9921388 5.2643827 10.217028 + 5900 5.0048643 4.7952641 8.9718929 + 5950 5.1843818 4.5987295 9.6858944 + 6000 5.0343993 4.946933 9.7436708 + 6050 4.6202714 5.3502658 10.752915 + 6100 5.6914422 5.3621964 10.281827 + 6150 5.1928763 5.9652686 10.923881 + 6200 5.0030409 5.2013891 10.056308 + 6250 4.9699876 5.2363753 9.9964211 + 6300 4.9129606 4.4558458 9.0419952 + 6350 4.6623958 4.4078264 8.528649 + 6400 4.9811441 5.1183207 10.261751 + 6450 5.3644017 5.5153937 10.401295 + 6500 5.6674981 5.7427566 11.928777 + 6550 5.1622364 5.3212928 10.067198 + 6600 4.5954278 5.1645397 10.16724 + 6650 4.9192712 5.0413326 9.95656 + 6700 4.6179845 4.5656214 9.3798952 + 6750 4.7287495 4.5071148 8.7890116 + 6800 4.8600442 4.8083512 10.245595 + 6850 5.0515531 5.1609272 10.553855 + 6900 5.1159742 5.1359869 10.594699 + 6950 4.8908884 5.0592418 9.5698704 + 7000 4.7654136 4.7530776 8.9439321 + 7050 4.779293 4.7534957 9.7244349 + 7100 5.2265831 5.6869073 10.32717 + 7150 5.4019177 5.15174 10.457567 + 7200 4.9817102 5.0596098 10.337574 + 7250 5.1836654 5.6065238 10.723108 + 7300 4.2916569 4.457143 8.5419099 + 7350 4.3906104 4.5439294 9.0805415 + 7400 4.998572 5.3386063 10.491418 + 7450 5.1109022 5.0506801 10.636116 + 7500 5.0248381 5.019932 10.217023 + 7550 5.0109265 5.1438717 9.9032426 + 7600 4.6628614 4.6204146 8.9459669 + 7650 4.8930717 5.0650009 10.049331 + 7700 4.9373454 5.6265835 10.210644 + 7750 5.5001067 5.3133253 10.667995 + 7800 5.0816102 5.0125753 10.591986 + 7850 4.9638046 5.1969015 9.9728333 + 7900 4.8438207 4.9217213 8.9978809 + 7950 4.7318805 4.6248537 8.6806596 + 8000 5.2808543 5.2892613 10.932535 + 8050 5.9609722 5.87087 10.47602 + 8100 5.2190231 5.6693244 11.244536 + 8150 5.3481127 5.2849903 10.222845 + 8200 4.7833053 4.7404657 9.2034474 + 8250 4.5461994 4.510467 10.294452 + 8300 4.6025175 4.8332817 8.7967546 + 8350 5.0389897 5.6642908 10.243402 + 8400 4.8414338 4.8925143 9.3653631 + 8450 5.5087429 4.7830361 10.831666 + 8500 5.2678146 5.1697789 9.9105782 + 8550 5.1211843 4.9097801 9.4165956 + 8600 5.8239149 5.0821022 10.803261 + 8650 5.3620154 5.5831747 11.16202 + 8700 5.1625813 4.8791404 10.537681 + 8750 4.5622461 5.0157549 10.013227 + 8800 4.4051517 5.0224553 9.6364273 + 8850 4.1711629 4.635617 8.5470244 + 8900 4.7049907 5.2458435 10.100728 + 8950 4.8568883 5.2360772 9.2306469 + 9000 5.0091899 5.2203574 10.718541 + 9050 5.1037824 4.9022451 10.24271 + 9100 5.0789015 4.9331454 9.173614 + 9150 5.3865455 5.3427553 11.40199 + 9200 5.5089482 5.9423232 10.976063 + 9250 5.1353552 5.0650262 10.040607 + 9300 4.6761948 4.9155175 9.6413722 + 9350 4.4780834 4.3934708 8.7049819 + 9400 4.2561799 4.7906324 9.046134 + 9450 5.6162819 5.2881846 9.9040868 + 9500 5.7554547 5.6111262 10.23849 + 9550 5.4230462 5.5656045 10.908006 + 9600 5.5045685 4.9818892 9.8929535 + 9650 5.0541481 5.0183351 9.5226021 + 9700 4.9712829 5.2395398 9.9996693 + 9750 5.0960017 5.4419775 10.914719 + 9800 5.0790688 5.6378474 10.00789 + 9850 4.9661747 5.114502 9.4585052 + 9900 5.0133498 4.7456254 9.4572653 + 9950 5.3318846 4.6643122 10.096292 + 10000 5.2227687 4.8924305 9.5894615 +Loop time of 4.78247 on 1 procs for 10000 steps with 500 atoms -Performance: 1152718.368 tau/day, 2668.330 timesteps/s -99.4% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 903298.340 tau/day, 2090.968 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 | 0.64903 | 0.64903 | 0.64903 | 0.0 | 17.32 -Neigh | 2.2534 | 2.2534 | 2.2534 | 0.0 | 60.13 -Comm | 0.22293 | 0.22293 | 0.22293 | 0.0 | 5.95 -Output | 0.0034931 | 0.0034931 | 0.0034931 | 0.0 | 0.09 -Modify | 0.53533 | 0.53533 | 0.53533 | 0.0 | 14.28 -Other | | 0.08346 | | | 2.23 +Pair | 0.73894 | 0.73894 | 0.73894 | 0.0 | 15.45 +Neigh | 2.9092 | 2.9092 | 2.9092 | 0.0 | 60.83 +Comm | 0.32306 | 0.32306 | 0.32306 | 0.0 | 6.76 +Output | 0.003392 | 0.003392 | 0.003392 | 0.0 | 0.07 +Modify | 0.6959 | 0.6959 | 0.6959 | 0.0 | 14.55 +Other | | 0.112 | | | 2.34 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 919 ave 919 max 919 min +Nghost: 905 ave 905 max 905 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3662 ave 3662 max 3662 min +Neighs: 3340 ave 3340 max 3340 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 3662 -Ave neighs/atom = 7.324 -Neighbor list builds = 4480 +Total # of neighbors = 3340 +Ave neighs/atom = 6.68 +Neighbor list builds = 4580 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:03 +Total wall time: 0:00:04 diff --git a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 index 2e2d9989dd..9be4413a96 100644 --- a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 +++ b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 @@ -52,233 +52,233 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 2.71 | 2.71 | 2.71 Mbytes Step c_1_press[1] c_1_press[2] c_1_press[3] 0 6.3937851 7.0436438 6.4461087 - 50 8.656807 7.9950197 15.884241 - 100 11.492654 12.329741 17.658703 - 150 8.6981119 8.6206624 14.114117 - 200 6.1456927 6.4457399 11.199275 - 250 5.5832485 5.5648091 10.400142 - 300 6.1328799 6.3010248 12.010437 - 350 7.1731722 7.5434426 14.588724 - 400 9.3347098 8.6490053 16.710495 - 450 9.5796766 8.9745197 18.230488 - 500 8.4810279 7.6334377 15.050771 - 550 6.5621497 7.401369 12.711355 - 600 6.5868791 6.4912059 13.361745 - 650 7.8188208 7.1180707 14.27939 - 700 7.6714427 7.8664221 14.845323 - 750 7.1545214 8.1596642 14.255973 - 800 8.1950867 8.6441653 15.642584 - 850 8.5624856 8.4004153 15.303218 - 900 7.2513726 7.522694 12.951416 - 950 6.9147537 7.4166804 13.712135 - 1000 7.9356647 7.9447497 14.787788 - 1050 8.0049909 8.3262071 15.736553 - 1100 7.47785 7.8850623 15.063921 - 1150 7.5982542 7.3264305 14.300792 - 1200 7.7141298 7.2955704 14.347839 - 1250 7.421808 7.0057566 13.701565 - 1300 8.0349263 7.8960785 14.360692 - 1350 7.6034411 8.1859894 15.296327 - 1400 7.7403226 7.7959668 15.155558 - 1450 8.0224022 7.2883482 14.979638 - 1500 7.4472686 7.4123823 14.065575 - 1550 7.8838674 7.3268327 14.0089 - 1600 7.7051065 7.6970609 15.025602 - 1650 8.3761114 7.8808173 16.143239 - 1700 7.8493638 7.9974325 15.369229 - 1750 6.7616091 6.9586731 13.253666 - 1800 6.7881829 6.4387333 13.293849 - 1850 7.4819924 8.113677 15.259022 - 1900 7.7619407 7.345373 14.252099 - 1950 9.1160797 8.6024027 16.442885 - 2000 8.8133522 8.1946233 15.676227 - 2050 7.9252468 7.5817269 14.615024 - 2100 7.3824657 7.2766684 15.063532 - 2150 6.8894956 6.7372708 13.607409 - 2200 7.039392 6.685916 13.545476 - 2250 8.0218429 7.5526941 15.263216 - 2300 8.0069299 7.9230893 16.349675 - 2350 7.8564415 8.2913478 14.62257 - 2400 7.4027437 7.0289244 14.244477 - 2450 8.1596868 6.9974968 13.956696 - 2500 7.3792516 6.7751363 13.897864 - 2550 8.7661201 7.9457114 15.3879 - 2600 8.3077502 7.4606043 15.518229 - 2650 7.5270266 8.1888278 14.833414 - 2700 7.9433204 7.872351 15.415577 - 2750 6.9284646 7.2785928 14.175083 - 2800 7.5239578 7.4370418 13.774583 - 2850 6.8456524 7.1993417 13.82663 - 2900 7.9547454 7.8797239 14.967569 - 2950 8.1366854 7.989168 15.722064 - 3000 7.7915591 7.7902194 14.887574 - 3050 8.3076915 8.5022034 15.966604 - 3100 7.3679745 7.2951683 15.032507 - 3150 6.3983597 7.1922179 14.248095 - 3200 7.3135998 7.6677326 14.588216 - 3250 7.7051677 7.4126323 13.935215 - 3300 7.8377055 7.7808126 15.481713 - 3350 8.4304815 8.5666028 14.52102 - 3400 8.090996 7.722647 15.150921 - 3450 8.3389456 7.5739975 14.33015 - 3500 7.6623037 7.2930598 14.361376 - 3550 7.6117545 6.9106485 13.851755 - 3600 7.1508283 7.6269826 13.535534 - 3650 7.4910852 7.9176295 15.691413 - 3700 8.4802801 8.6324769 16.762136 - 3750 7.022402 7.3282804 14.110888 - 3800 7.5627539 7.0503911 14.55662 - 3850 7.2787215 7.2608067 15.046768 - 3900 7.5355799 6.4532442 14.167082 - 3950 8.048962 7.8525579 15.059109 - 4000 7.3175513 8.1005178 14.269317 - 4050 7.520408 8.2682863 14.522748 - 4100 7.6146474 7.7910616 15.199754 - 4150 7.3099191 7.3588162 14.685704 - 4200 7.7659083 7.2886996 14.33525 - 4250 7.5326919 7.4415236 13.874457 - 4300 7.6950275 8.0507821 14.302796 - 4350 7.7170173 8.8246914 14.911061 - 4400 8.0055097 8.4924898 16.225929 - 4450 7.4405645 8.6425584 14.0991 - 4500 6.4050093 6.813939 13.138703 - 4550 6.47962 7.1644972 14.236311 - 4600 7.8672141 7.2404922 15.653959 - 4650 8.1942529 7.4061361 14.232369 - 4700 7.8827633 7.9150952 15.400505 - 4750 7.5095565 7.5093531 15.016387 - 4800 7.75753 7.5830004 14.189254 - 4850 7.840715 7.4954187 15.121937 - 4900 7.5058956 7.5009855 13.389342 - 4950 7.9778116 7.5810052 14.869835 - 5000 8.0941013 7.5222021 15.321999 - 5050 8.6041139 8.3498159 16.208856 - 5100 7.8357702 7.8500124 14.954782 - 5150 8.1036917 7.5357815 15.714879 - 5200 7.4868525 7.4885485 14.167469 - 5250 6.9392666 6.3711563 13.014779 - 5300 7.7294001 7.5681854 14.60363 - 5350 8.2947591 7.5597033 15.076707 - 5400 7.8365134 8.3559985 14.451289 - 5450 7.6577176 7.8573581 14.649332 - 5500 7.6344288 7.6731281 14.411212 - 5550 7.2854884 7.2377463 14.580478 - 5600 7.6332558 7.5037409 14.809068 - 5650 7.2491454 7.5479013 15.196638 - 5700 7.5027918 8.0434388 14.006705 - 5750 8.4679702 7.2893309 15.600406 - 5800 8.11675 8.7790839 15.150116 - 5850 7.8571033 7.1044939 14.730559 - 5900 7.4555155 6.8841813 13.743156 - 5950 7.4269873 7.4363562 13.722307 - 6000 7.014144 7.2841802 14.010536 - 6050 8.2802859 8.741796 16.724881 - 6100 7.9607544 8.2594316 14.965005 - 6150 7.7505098 7.6437264 14.941281 - 6200 7.2637841 7.2845655 14.922083 - 6250 7.4781943 7.3184749 14.627774 - 6300 7.0053246 7.6973025 14.77968 - 6350 6.9682271 7.2193417 13.261589 - 6400 7.6344736 7.5178683 15.586197 - 6450 8.1803746 8.9186636 15.298001 - 6500 7.9535931 8.0466048 15.058292 - 6550 8.056327 8.7108507 15.645091 - 6600 7.3980755 7.087917 13.188502 - 6650 7.3835052 7.2608077 13.95146 - 6700 7.65293 7.0795957 13.742847 - 6750 7.3562754 7.9842502 14.9349 - 6800 8.2494698 8.1508069 15.314676 - 6850 8.1303284 7.8202726 14.50709 - 6900 6.8743362 7.177725 13.485731 - 6950 7.9101459 7.9096716 14.503653 - 7000 7.8164436 8.3236187 16.081817 - 7050 7.7467975 8.7347369 14.9306 - 7100 7.7324222 7.1489428 14.130705 - 7150 6.7791769 6.9011542 14.121399 - 7200 7.6561999 7.5106057 15.234413 - 7250 8.1336506 8.2347678 15.24865 - 7300 6.9098706 7.1934869 14.762268 - 7350 7.1656572 7.7495163 13.867435 - 7400 7.4777956 7.0012888 14.888226 - 7450 8.3176523 7.7845549 15.400925 - 7500 8.2660801 7.5249967 15.313452 - 7550 7.8682936 7.2724016 15.760637 - 7600 7.3975227 7.5654528 13.588662 - 7650 6.7264804 7.1183131 13.219998 - 7700 7.5072355 7.5540796 15.22008 - 7750 7.7421897 8.0113389 14.385238 - 7800 7.6120438 7.9292888 14.66559 - 7850 8.1731646 7.7092319 15.005626 - 7900 8.2285993 8.0637538 15.54714 - 7950 7.7466424 8.3179588 15.10088 - 8000 6.9988726 7.2092201 12.502859 - 8050 7.0919479 7.0585849 14.613424 - 8100 8.0428791 7.8888417 15.945665 - 8150 8.5677024 8.6618742 15.592526 - 8200 7.5972541 7.6902215 14.030522 - 8250 6.8185307 7.1945156 14.452569 - 8300 7.6384046 7.9698235 13.64607 - 8350 7.8378987 7.547662 15.437631 - 8400 8.2496937 7.8279926 14.684647 - 8450 7.5583846 7.5449624 13.393606 - 8500 7.9690263 7.4398188 15.172533 - 8550 8.9148619 8.1181912 14.965998 - 8600 7.9055582 7.8323691 14.778383 - 8650 7.846331 7.3302071 13.812249 - 8700 7.2669615 6.9949093 14.232954 - 8750 7.7494364 7.4431371 13.748379 - 8800 7.9660017 7.6941365 14.366261 - 8850 7.6599154 7.8343017 14.753737 - 8900 7.623307 7.5207726 15.324822 - 8950 7.4784899 7.7901163 15.290832 - 9000 7.93144 8.1349231 16.08637 - 9050 7.7550193 7.6966669 14.554758 - 9100 7.7952657 7.6029648 13.828782 - 9150 7.2915866 7.2140714 13.882209 - 9200 6.8619177 7.2210075 13.702975 - 9250 8.0756482 7.5893593 15.954582 - 9300 8.022774 7.5747016 14.507683 - 9350 7.4993526 8.1111805 14.917379 - 9400 8.8254745 8.0723829 15.717736 - 9450 7.1983725 7.6626286 13.97487 - 9500 7.0602895 7.6733732 13.883137 - 9550 6.5519083 7.4242978 13.607039 - 9600 8.4732891 7.4177194 15.533846 - 9650 8.9193417 8.5982503 16.110043 - 9700 7.8935173 7.8222315 14.42615 - 9750 7.2393047 7.545224 14.557362 - 9800 6.8495209 7.0841522 13.812737 - 9850 6.9791315 7.5743519 13.013286 - 9900 7.4984681 7.8699746 14.977208 - 9950 8.2030761 8.9314031 17.23834 - 10000 9.3670418 8.2034985 15.902349 -Loop time of 1.5138 on 4 procs for 10000 steps with 500 atoms + 50 7.9020345 7.303289 14.733929 + 100 8.3214325 8.385843 13.166247 + 150 5.7168419 5.6083988 9.7224198 + 200 3.8875348 4.0840705 7.9912973 + 250 4.2933724 4.2410519 7.7200953 + 300 4.5452314 4.2434949 8.6709832 + 350 5.446489 5.6166962 11.300536 + 400 6.0682558 5.7787878 12.106852 + 450 5.3884296 5.5066688 9.9100012 + 500 4.8046418 4.7115986 9.9769201 + 550 4.9043933 4.6240966 9.319336 + 600 4.6843238 4.9571246 9.5325487 + 650 5.1952989 5.195648 9.6187047 + 700 5.4163364 5.2938289 10.136655 + 750 5.6723178 5.0670261 11.415221 + 800 5.9379901 5.6402916 10.815209 + 850 5.0695389 5.3021432 10.742859 + 900 4.6498961 4.7111912 9.8453524 + 950 4.4811637 5.1701321 9.4217645 + 1000 4.750149 4.2420768 9.3510788 + 1050 4.5973376 5.2046787 9.8633025 + 1100 4.7879517 4.9051339 9.8658578 + 1150 5.0528775 5.5048671 10.110905 + 1200 4.9926841 5.2482049 9.9610519 + 1250 4.8475836 4.8499116 9.5753651 + 1300 5.2930219 5.0593566 10.869335 + 1350 5.4722342 5.0830411 10.693439 + 1400 4.8165803 4.9851498 10.04213 + 1450 4.6276458 4.5642988 9.2306141 + 1500 5.0196773 4.5470773 8.7204145 + 1550 4.878246 5.1583406 10.263895 + 1600 5.4921049 5.3126759 10.274755 + 1650 5.4363266 5.1708866 9.9880665 + 1700 4.9186005 5.2841155 9.5911223 + 1750 4.9105668 4.7112031 8.9221295 + 1800 4.9833291 4.886821 9.6573393 + 1850 5.0729703 4.8331712 10.094971 + 1900 5.7220173 5.9330299 10.580261 + 1950 5.3176022 5.7140521 11.11604 + 2000 5.3247727 5.5172893 10.622834 + 2050 5.2055235 4.8768078 9.9819356 + 2100 4.4604981 4.1427844 7.8106592 + 2150 4.4406592 4.8264893 9.6662695 + 2200 5.2350836 5.1039145 10.36006 + 2250 5.3777857 5.3274609 11.357157 + 2300 5.4888334 5.9555482 10.76346 + 2350 4.6122564 4.7356468 9.0833059 + 2400 4.6670237 4.4895588 9.0619648 + 2450 4.2201177 4.2558397 9.4898835 + 2500 5.452448 5.4336384 10.50224 + 2550 5.012581 5.316158 10.324517 + 2600 5.0880279 5.1264772 10.085103 + 2650 4.8885834 5.2368982 9.6002032 + 2700 5.1549266 5.3419678 11.335447 + 2750 5.497105 5.3643445 9.9990393 + 2800 4.8826744 4.9875712 10.125435 + 2850 4.8617121 5.1282348 9.5629401 + 2900 4.7883446 4.6187804 9.0562496 + 2950 4.7656266 5.1293592 10.693811 + 3000 5.2676745 5.110172 9.3512146 + 3050 4.5749222 4.8413907 10.311305 + 3100 5.0794819 5.265009 9.1598496 + 3150 5.2078869 5.1879882 10.412548 + 3200 5.0187616 4.6226213 9.7266174 + 3250 5.1541897 4.5157063 9.8355764 + 3300 5.0721396 5.3545282 10.174356 + 3350 5.3984495 5.3222207 10.008886 + 3400 5.1263226 5.1189192 10.361534 + 3450 5.1251845 4.8312752 9.6546597 + 3500 5.1133696 5.2646289 10.320765 + 3550 4.9884235 5.3861707 9.1944042 + 3600 5.196909 5.203186 10.085965 + 3650 5.4717592 5.2205442 10.251283 + 3700 5.4429771 5.3027898 11.385714 + 3750 5.5688484 5.5980199 10.558193 + 3800 4.5239453 4.7021545 8.952588 + 3850 4.6438079 4.6409958 9.3890154 + 3900 5.1108473 4.8787691 10.665694 + 3950 5.6398426 5.4386578 10.668189 + 4000 5.063697 4.9663173 10.513266 + 4050 4.8770847 4.4603573 9.8101845 + 4100 4.3950768 4.3579384 8.3402845 + 4150 4.3355402 5.0429352 10.323111 + 4200 4.7688478 5.051487 9.0632339 + 4250 4.9879366 5.3367146 10.409554 + 4300 5.4578199 5.4889206 10.418789 + 4350 5.6598068 5.4538572 10.842349 + 4400 5.3705312 5.3796871 10.430547 + 4450 4.663804 5.058851 9.2705923 + 4500 4.3439039 4.3523422 8.1747925 + 4550 4.5414802 4.3750772 9.2702452 + 4600 4.9216199 5.2897069 10.747727 + 4650 5.5154852 5.9628437 10.5168 + 4700 5.45199 5.382787 10.654544 + 4750 4.7525419 5.4701385 9.3189378 + 4800 5.3696365 4.6134207 9.4455676 + 4850 5.2444123 5.035993 9.4148435 + 4900 5.6006507 4.8536828 10.283579 + 4950 5.155711 4.978634 10.58973 + 5000 5.0854607 4.9853307 9.2414296 + 5050 5.1098462 4.7349164 9.8739001 + 5100 5.1989395 5.0217416 9.8780949 + 5150 5.612116 5.2165007 10.338464 + 5200 5.0571356 5.3109846 10.685262 + 5250 5.4832657 5.0371665 8.9420853 + 5300 4.5312549 4.9629392 8.2478064 + 5350 5.1617038 5.0533699 10.452218 + 5400 5.7873394 5.6776926 11.926526 + 5450 5.7002516 5.243239 10.940265 + 5500 4.7896799 4.898544 10.163856 + 5550 4.9155627 4.9567495 9.4445476 + 5600 4.2447343 4.5045912 8.7732992 + 5650 5.070197 4.7343938 9.9908239 + 5700 4.9609446 5.0901934 10.812786 + 5750 5.4001631 5.5552888 10.085896 + 5800 5.4209837 4.7153245 9.6865245 + 5850 4.9801041 5.180338 9.8930439 + 5900 5.3423595 5.2341361 10.294159 + 5950 5.683047 5.6830131 10.24313 + 6000 5.0618789 5.4533644 10.713412 + 6050 5.4034888 4.6341621 10.031976 + 6100 5.1934299 4.7525347 9.1287151 + 6150 5.0092398 4.806931 10.024305 + 6200 5.3046516 5.3083532 9.6396223 + 6250 5.2824046 4.7957557 10.305279 + 6300 5.3007029 5.0071874 11.175322 + 6350 5.1128883 4.990408 9.3439118 + 6400 5.0543602 4.9971378 9.8259954 + 6450 4.8843692 4.9116343 10.08132 + 6500 4.5966453 4.8042861 9.160272 + 6550 4.8510961 4.7096646 9.8009968 + 6600 5.658307 5.2330511 10.739519 + 6650 5.2374409 5.3241249 10.291779 + 6700 4.9006975 5.0036186 9.9872029 + 6750 5.2209104 5.1826025 9.5671875 + 6800 4.5238727 4.3070529 8.6072303 + 6850 4.2617247 4.7551571 9.7302077 + 6900 5.6499354 4.8714257 10.723511 + 6950 5.6881769 5.1800721 10.18134 + 7000 5.588834 5.0104896 10.304105 + 7050 4.9404045 4.8589121 9.7096741 + 7100 5.2208179 4.9339808 9.7737491 + 7150 5.4507842 5.046485 10.734783 + 7200 4.9737171 5.5760486 9.1627431 + 7250 4.5967409 4.750471 9.315832 + 7300 5.5147308 5.3202861 10.542679 + 7350 5.7730418 5.5363574 10.384376 + 7400 4.9879586 5.2837443 9.4485798 + 7450 5.1862431 4.8357842 10.017598 + 7500 5.4528245 5.1864957 10.941774 + 7550 5.4202434 5.1089468 10.128264 + 7600 4.8063537 4.8723653 9.0364984 + 7650 4.3144701 4.6148377 9.4939315 + 7700 4.9033831 5.5327473 9.9054613 + 7750 5.0693093 5.0768222 10.473081 + 7800 5.0591805 5.6009473 10.006225 + 7850 5.15269 5.468248 10.404619 + 7900 5.1971759 5.0615117 9.9614488 + 7950 4.9771238 4.886213 9.4730722 + 8000 4.7731123 5.1111433 9.9550597 + 8050 5.1655183 5.4432364 9.6649669 + 8100 5.4597006 5.4026039 11.631184 + 8150 5.3229643 5.4394219 9.9830611 + 8200 4.5420712 4.9359646 9.0121988 + 8250 4.5455108 4.3883996 10.304568 + 8300 5.219721 5.1571958 10.305462 + 8350 4.7291561 4.7391636 9.0768372 + 8400 5.3262934 5.8221591 11.065466 + 8450 4.7583026 5.2282086 10.291955 + 8500 4.9174536 4.5701979 10.140444 + 8550 4.459922 4.8293188 9.4438719 + 8600 4.7962584 4.5811071 9.5158666 + 8650 4.6097275 4.431952 9.4350505 + 8700 5.166554 5.2000584 11.162202 + 8750 5.2353596 5.1668944 10.829751 + 8800 5.3150111 4.9983333 9.8402224 + 8850 4.9571197 4.9196589 9.4880549 + 8900 4.902223 4.7539187 10.002425 + 8950 4.9531983 5.0517321 9.7838444 + 9000 5.4003802 4.9900303 10.550808 + 9050 4.9254643 5.0678701 10.24321 + 9100 4.9902263 4.9056928 9.0326566 + 9150 5.1003677 5.1555374 10.049056 + 9200 5.2358131 5.5834504 10.354698 + 9250 5.5781649 5.1188429 10.361369 + 9300 5.2100192 5.0737267 10.074694 + 9350 5.1462976 4.8010759 9.0279769 + 9400 5.0177693 5.4890092 10.03612 + 9450 5.2507957 5.541141 10.639854 + 9500 5.836784 4.9498236 10.288015 + 9550 5.4698183 5.8761209 10.979924 + 9600 5.0534023 5.0043428 10.436057 + 9650 4.3619773 4.5413125 9.047513 + 9700 4.3777508 4.7902251 8.9501908 + 9750 4.6851974 4.3152085 8.825764 + 9800 5.7312665 4.850913 10.247637 + 9850 6.2290614 5.5480801 10.934907 + 9900 6.0316892 6.1098926 11.562223 + 9950 5.6370814 5.3933342 11.148805 + 10000 4.6429923 5.0853156 9.4267693 +Loop time of 3.06414 on 4 procs for 10000 steps with 500 atoms -Performance: 2853736.392 tau/day, 6605.871 timesteps/s -98.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 1409858.531 tau/day, 3263.561 timesteps/s +99.4% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.16778 | 0.17518 | 0.17885 | 1.0 | 11.57 -Neigh | 0.55898 | 0.57272 | 0.59026 | 1.6 | 37.83 -Comm | 0.31971 | 0.33993 | 0.36759 | 3.1 | 22.46 -Output | 0.003036 | 0.0033901 | 0.0042133 | 0.8 | 0.22 -Modify | 0.34512 | 0.35303 | 0.35965 | 0.9 | 23.32 -Other | | 0.06956 | | | 4.60 +Pair | 0.27954 | 0.30916 | 0.3866 | 8.1 | 10.09 +Neigh | 1.0657 | 1.129 | 1.2853 | 8.5 | 36.85 +Comm | 0.56334 | 0.80526 | 0.89816 | 15.6 | 26.28 +Output | 0.0032749 | 0.0041527 | 0.006541 | 2.1 | 0.14 +Modify | 0.6522 | 0.67016 | 0.69843 | 2.1 | 21.87 +Other | | 0.1464 | | | 4.78 -Nlocal: 125 ave 132 max 121 min -Histogram: 2 0 0 0 1 0 0 0 0 1 -Nghost: 478 ave 488 max 470 min -Histogram: 1 1 0 0 0 0 1 0 0 1 -Neighs: 915.25 ave 981 max 889 min -Histogram: 3 0 0 0 0 0 0 0 0 1 +Nlocal: 125 ave 130 max 122 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Nghost: 459.75 ave 470 max 448 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 837 ave 867 max 811 min +Histogram: 2 0 0 0 0 0 0 0 1 1 -Total # of neighbors = 3661 -Ave neighs/atom = 7.322 -Neighbor list builds = 4485 +Total # of neighbors = 3348 +Ave neighs/atom = 6.696 +Neighbor list builds = 4589 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:01 +Total wall time: 0:00:03 From b34109af602fc2988e1eba592155ab37c9389595 Mon Sep 17 00:00:00 2001 From: David Nicholson Date: Mon, 2 Oct 2017 23:43:31 -0400 Subject: [PATCH 18/21] formatting changes --- src/USER-UEF/compute_pressure_uef.cpp | 27 ++++++++++++--------------- src/USER-UEF/compute_temp_uef.cpp | 10 +++------- 2 files changed, 15 insertions(+), 22 deletions(-) diff --git a/src/USER-UEF/compute_pressure_uef.cpp b/src/USER-UEF/compute_pressure_uef.cpp index 5c6ef0940f..43054d7d3f 100644 --- a/src/USER-UEF/compute_pressure_uef.cpp +++ b/src/USER-UEF/compute_pressure_uef.cpp @@ -38,12 +38,12 @@ using namespace LAMMPS_NS; * ----------------------------------------------------------------------*/ ComputePressureUef::ComputePressureUef(LAMMPS *lmp, int narg, char **arg) : ComputePressure(lmp, narg, arg) - { - ext_flags[0] = true; - ext_flags[1] = true; - ext_flags[2] = true; - in_fix=false; - } +{ + ext_flags[0] = true; + ext_flags[1] = true; + ext_flags[2] = true; + in_fix=false; +} /* ---------------------------------------------------------------------- * Check for the uef fix @@ -54,8 +54,7 @@ void ComputePressureUef::init() // check to make sure the other uef fix is on // borrowed from Pieter's nvt/sllod code int i=0; - for (i=0; infix; i++) - { + for (i=0; infix; i++) { if (strcmp(modify->fix[i]->style,"nvt/uef")==0) break; if (strcmp(modify->fix[i]->style,"npt/uef")==0) @@ -87,18 +86,15 @@ double ComputePressureUef::compute_scalar() int k =0; scalar = 0; - if (ext_flags[0]) - { + if (ext_flags[0]) { scalar += vector[0]; k++; } - if (ext_flags[1]) - { + if (ext_flags[1]) { scalar += vector[1]; k++; } - if (ext_flags[2]) - { + if (ext_flags[2]) { scalar += vector[2]; k++; } @@ -179,9 +175,11 @@ void ComputePressureUef::virial_rot(double *x, const double r[3][3]) { double t[3][3]; + // [00 10 20 ] [ 0 3 4 ] [00 01 02 ] // [01 11 21 ] [ 3 1 5 ] [10 11 12 ] // [02 12 22 ] [ 4 5 2 ] [20 21 22 ] + for (int k = 0; k<3; ++k) { t[0][k] = x[0]*r[0][k] + x[3]*r[1][k] + x[4]*r[2][k]; @@ -195,4 +193,3 @@ void ComputePressureUef::virial_rot(double *x, const double r[3][3]) x[5] = r[0][1]*t[0][2] + r[1][1]*t[1][2] + r[2][1]*t[2][2]; x[2] = r[0][2]*t[0][2] + r[1][2]*t[1][2] + r[2][2]*t[2][2]; } - diff --git a/src/USER-UEF/compute_temp_uef.cpp b/src/USER-UEF/compute_temp_uef.cpp index 2947adc879..6055524056 100644 --- a/src/USER-UEF/compute_temp_uef.cpp +++ b/src/USER-UEF/compute_temp_uef.cpp @@ -42,8 +42,7 @@ void ComputeTempUef::init() // check to make sure the other uef fix is on // borrowed from Pieter's nvt/sllod code int i=0; - for (i=0; infix; i++) - { + for (i=0; infix; i++) { if (strcmp(modify->fix[i]->style,"nvt/uef")==0) break; if (strcmp(modify->fix[i]->style,"npt/uef")==0) @@ -61,8 +60,7 @@ void ComputeTempUef::init() void ComputeTempUef::compute_vector() { ComputeTemp::compute_vector(); - if (rot_flag) - { + if (rot_flag) { double rot[3][3]; ( (FixNHUef*) modify->fix[ifix_uef])->get_rot(rot); virial_rot(vector,rot); @@ -94,8 +92,7 @@ void ComputeTempUef::virial_rot(double *x, const double r[3][3]) // [00 10 20 ] [ 0 3 4 ] [00 01 02 ] // [01 11 21 ] [ 3 1 5 ] [10 11 12 ] // [02 12 22 ] [ 4 5 2 ] [20 21 22 ] - for (int k = 0; k<3; ++k) - { + for (int k = 0; k<3; ++k) { t[0][k] = x[0]*r[0][k] + x[3]*r[1][k] + x[4]*r[2][k]; t[1][k] = x[3]*r[0][k] + x[1]*r[1][k] + x[5]*r[2][k]; t[2][k] = x[4]*r[0][k] + x[5]*r[1][k] + x[2]*r[2][k]; @@ -107,4 +104,3 @@ void ComputeTempUef::virial_rot(double *x, const double r[3][3]) x[5] = r[0][1]*t[0][2] + r[1][1]*t[1][2] + r[2][1]*t[2][2]; x[2] = r[0][2]*t[0][2] + r[1][2]*t[1][2] + r[2][2]*t[2][2]; } - From af1fc45db0b35b9809de4e5fee0724faffe4efbf Mon Sep 17 00:00:00 2001 From: David Nicholson Date: Tue, 3 Oct 2017 00:04:52 -0400 Subject: [PATCH 19/21] added citation to doc --- doc/src/fix_nh_uef.txt | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt index 9cee428d83..dfb40dfb76 100644 --- a/doc/src/fix_nh_uef.txt +++ b/doc/src/fix_nh_uef.txt @@ -42,9 +42,11 @@ Simulations under extensional flow may be carried out for an indefinite amount of time. It is an implementation of the boundary conditions from "(Dobson)"_#Dobson, and also uses numerical lattice reduction as was proposed by "(Hunt)"_#Hunt. The lattice reduction algorithm is from -"(Semaev)"_Semaev. The package is intended for simulations of +"(Semaev)"_Semaev. The fix is intended for simulations of homogeneous flows, and integrates the SLLOD equations of motion, originally proposed by Hoover and Ladd (see "(Evans and Morriss)"_#Sllod). +Additional detail about this implementation can be found in +"(Nicholson and Rutledge)"_#Nicholson. The applied flow field is set by the {eps} keyword. The values {edot_x} and {edot_y} correspond to the strain rates in the xx and yy directions. @@ -204,3 +206,6 @@ The reason for this change is given in "fix nvt/sllod"_fix_nvt_sllod.html. :link(Sllod) [(Evans and Morriss)] Evans and Morriss, Phys Rev A, 30, 1528 (1984). + +:link(Nicholson) +[(Nicholson and Rutledge)] Nicholson and Rutledge, J Chem Phys, 145, 244903 (2016). From 11eed234f08ab0b060840f8aa4db7d603e0cc4d5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 3 Oct 2017 00:14:34 -0400 Subject: [PATCH 20/21] include dump cfg/uef in commands toctree --- doc/src/commands.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/src/commands.txt b/doc/src/commands.txt index 06752f6960..5fb06f2011 100644 --- a/doc/src/commands.txt +++ b/doc/src/commands.txt @@ -32,6 +32,7 @@ Commands :h1 dimension displace_atoms dump + dump_cfg_uef dump_h5md dump_image dump_modify From 0f5d7dcc0f537cf2bb756c9350c358fea13bc99e Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Sat, 7 Oct 2017 12:38:41 -0600 Subject: [PATCH 21/21] cmake: added USER-UEF --- cmake/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 2cc11d4ecb..967f229759 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -105,7 +105,7 @@ set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD - USER-SMTBQ USER-SPH USER-TALLY USER-VTK USER-QUIP USER-QMMM) + USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) foreach(PKG ${DEFAULT_PACKAGES}) option(ENABLE_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})