diff --git a/doc/src/Howto_bpm.rst b/doc/src/Howto_bpm.rst index 893486c989..63625fe793 100644 --- a/doc/src/Howto_bpm.rst +++ b/doc/src/Howto_bpm.rst @@ -97,10 +97,10 @@ This also requires a unique integrator :doc:`fix nve/sphere/bpm to :doc:`fix nve/asphere `. To monitor the fracture of bonds in the system, all BPM bond styles -can be associated with an instance of :doc:`fix store/local -` to record all instances of bond breakage for -output. Additionally, one can use :doc:`compute nbond/atom -` to tally the current number of bonds per atom. +have the ability to record instances of bond breakage to output using +the :doc:`dump local ` command. Additionally, one can use +:doc:`compute nbond/atom ` to tally the current +number of bonds per atom. In addition to bond styles, a new pair style :doc:`pair bpm/spring ` was added to accompany the bpm/spring bond diff --git a/doc/src/bond_bpm_rotational.rst b/doc/src/bond_bpm_rotational.rst index fd6b448f24..ccd27b1327 100644 --- a/doc/src/bond_bpm_rotational.rst +++ b/doc/src/bond_bpm_rotational.rst @@ -14,12 +14,15 @@ Syntax .. parsed-literal:: - *store/local* values = ID of associated fix store/local followed by one or more attributes + *store/local* values = fix_ID N attributes ... + * fix_ID = ID of associated internal fix to store data + * N = prepare data for output every this many timesteps + * attributes = zero or more of the below attributes may be appended - *id1, id2* = IDs of 2 atoms in the bond - *time* = the timestep the bond broke - *x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units) - *x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units) + *id1, id2* = IDs of 2 atoms in the bond + *time* = the timestep the bond broke + *x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units) + *x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units) *overlay/pair* value = none bonded particles will still interact with pair forces @@ -32,7 +35,7 @@ Examples bond_style bpm/rotational bond_coeff 1 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.02 0.002 0.002 - bond_style bpm/rotational myfix time id1 id2 + bond_style bpm/rotational myfix 1000 time id1 id2 fix myfix all store/local 1000 3 dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3] dump_modify 1 write_header no @@ -132,15 +135,33 @@ the *overlay/pair* keyword. These settings require specific restrictions. Further details can be found in the `:doc: how to ` page on BPMs. -This bond style tracks broken bonds and can record them using an -instance of :doc:`fix store/local ` if the -*store/local* keyword is used followed by the ID of the fix and then a -series of bond attributes. +If the *store/local* keyword is used, this fix will track bonds that +break during the simulation. Whenever a bond breaks, data is processed +and transferred to an internal fix labeled *fix_ID*. This allows the +local data to be accessed by other LAMMPS commands. -Note that when bonds are dumped to a file via the :doc:`dump local ` -command, bonds with type 0 (broken bonds) are not included. The -:doc:`delete_bonds ` command can also be used to query the -status of broken bonds or permanently delete them, e.g.: +Following any optional keyword/value arguments, a list of one or more +attributes is specified. These include the IDs of the two atoms in +the bond. The other attributes for the two atoms include the timestep +during which the bond broke and the current/initial center of mass +position of the two atoms. + +This bond style tracks broken bonds and records the requested attributes. +Data is continuously accumulated over intervals of *N* +timesteps. At the end of each interval, all of the saved accumulated +data is deleted to make room for new data. Individual datum may +therefore persist anywhere between *1* to *N* timesteps depending on +when they are saved. This data can be accessed using the *fix_ID* and a +:doc:`dump local ` command. To ensure all data is output, +the dump frequency should correspond to the same interval of *N* +timesteps. A dump frequency of an integer multiple of *N* can be used +to regularly output a sample of the accumulated data. + +Note that when unbroken bonds are dumped to a file via the +:doc:`dump local ` command, bonds with type 0 (broken bonds) +are not included. +The :doc:`delete_bonds ` command can also be used to +query the status of broken bonds or permanently delete them, e.g.: .. code-block:: LAMMPS @@ -162,6 +183,22 @@ of a pairwise interaction, since energy is not conserved in these dissipative potentials. It also returns only the normal component of the pairwise interaction force. +The accumulated data is not written to restart files and should be +output before a restart file is written to avoid missing data. + +The internal fix calculates a local vector or local array depending on the +number of input values. The length of the vector or number of rows in +the array is the number of recorded, lost interactions. If a single +input is specified, a local vector is produced. If two or more inputs +are specified, a local array is produced where the number of columns = +the number of inputs. The vector or array can be accessed by any +command that uses local values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS +output options. + +The vector or array will be floating point values that correspond to +the specified attribute. + Restrictions """""""""""" @@ -189,8 +226,7 @@ The *bpm/rotational* style requires :doc:`atom style sphere/bpm `. Related commands """""""""""""""" -:doc:`bond_coeff `, :doc:`fix store/local `, -:doc:`fix nve/sphere/bpm ` +:doc:`bond_coeff `, :doc:`fix nve/sphere/bpm ` Default """"""" diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index 4bd73d6af0..164b1dbed4 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -14,12 +14,15 @@ Syntax .. parsed-literal:: - *store/local* values = ID of associated fix store/local followed by one or more attributes + *store/local* values = fix_ID N attributes ... + * fix_ID = ID of associated internal fix to store data + * N = prepare data for output every this many timesteps + * attributes = zero or more of the below attributes may be appended - *id1, id2* = IDs of 2 atoms in the bond - *time* = the timestep the bond broke - *x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units) - *x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units) + *id1, id2* = IDs of 2 atoms in the bond + *time* = the timestep the bond broke + *x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units) + *x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units) *overlay/pair* value = none bonded particles will still interact with pair forces @@ -32,8 +35,7 @@ Examples bond_style bpm/spring bond_coeff 1 1.0 0.05 0.1 - bond_style bpm/spring myfix time id1 id2 - fix myfix all store/local 1000 3 + bond_style bpm/spring myfix 1000 time id1 id2 dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3] dump_modify 1 write_header no @@ -96,13 +98,31 @@ the *overlay/pair* keyword. These settings require specific restrictions. Further details can be found in the `:doc: how to ` page on BPMs. -This bond style tracks broken bonds and can record them using an -instance of :doc:`fix store/local ` if the -*store/local* keyword is used followed by the ID of the fix and then a -series of bond attributes. +If the *store/local* keyword is used, this fix will track bonds that +break during the simulation. Whenever a bond breaks, data is processed +and transferred to an internal fix labeled *fix_ID*. This allows the +local data to be accessed by other LAMMPS commands. -Note that when bonds are dumped to a file via the :doc:`dump local -` command, bonds with type 0 (broken bonds) are not included. +Following any optional keyword/value arguments, a list of one or more +attributes is specified. These include the IDs of the two atoms in +the bond. The other attributes for the two atoms include the timestep +during which the bond broke and the current/initial center of mass +position of the two atoms. + +This bond style tracks broken bonds and records the requested attributes. +Data is continuously accumulated over intervals of *N* +timesteps. At the end of each interval, all of the saved accumulated +data is deleted to make room for new data. Individual datum may +therefore persist anywhere between *1* to *N* timesteps depending on +when they are saved. This data can be accessed using the *fix_ID* and a +:doc:`dump local ` command. To ensure all data is output, +the dump frequency should correspond to the same interval of *N* +timesteps. A dump frequency of an integer multiple of *N* can be used +to regularly output a sample of the accumulated data. + +Note that when unbroken bonds are dumped to a file via the +:doc:`dump local ` command, bonds with type 0 (broken bonds) +are not included. The :doc:`delete_bonds ` command can also be used to query the status of broken bonds or permanently delete them, e.g.: @@ -124,6 +144,22 @@ The single() function of these pair styles returns 0.0 for the energy of a pairwise interaction, since energy is not conserved in these dissipative potentials. +The accumulated data is not written to restart files and should be +output before a restart file is written to avoid missing data. + +The internal fix calculates a local vector or local array depending on the +number of input values. The length of the vector or number of rows in +the array is the number of recorded, lost interactions. If a single +input is specified, a local vector is produced. If two or more inputs +are specified, a local array is produced where the number of columns = +the number of inputs. The vector or array can be accessed by any +command that uses local values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS +output options. + +The vector or array will be floating point values that correspond to +the specified attribute. + Restrictions """""""""""" @@ -149,8 +185,7 @@ setting Related commands """""""""""""""" -:doc:`bond_coeff `, :doc:`fix store/local `, -:doc:`pair bpm/spring ` +:doc:`bond_coeff `, :doc:`pair bpm/spring ` Default """"""" diff --git a/doc/src/fix_store_local.rst b/doc/src/fix_store_local.rst deleted file mode 100644 index 0f0ebc5ce6..0000000000 --- a/doc/src/fix_store_local.rst +++ /dev/null @@ -1,97 +0,0 @@ -.. index:: fix store/local - -fix store/local command -======================== - -Syntax -"""""" - -.. parsed-literal:: - - fix ID group-ID store/local N nvalues - -* ID, group-ID are documented in :doc:`fix ` command -* store/local = style name of this fix command -* N = prepare data for output every this many timesteps -* nvalues = number of values stored by this fix - -Examples -"""""""" - -.. code-block:: LAMMPS - - bond_style bpm/simple store/local 1 id1 id2 - fix 1 all store/local 1000 2 - dump 1 all local 1000 dump.local f_1[1] f_1[2] - dump_modify 1 write_header no - - pair_style hybrid/overlay tracker 1 x y z lj/cut 2.5 - fix 1 all store/local 1000 3 - dump 1 all local 1000 dump.local f_1[1] f_1[2] f_1[3] - -Description -""""""""""" - -This fix provides the ability to store local data generated by another -LAMMPS command, including some pair and bond styles, so it can be -output. One examples, shown above, is the -:doc:`bpm/simple bondstyle ` which allows bonds to -break and passes information on the broken bonds to this fix. A -:doc:`dump local ` command can then output the list of -broken bonds - -This fix continuously accumulates local data over intervals of *N* -timesteps. At the end of each interval, all of the saved accumulated -data is deleted to make room for new data. Individual datum may -therefore persist anywhere between *1* to *N* timesteps depending on -when they are saved. This data can be accessed by a -:doc:`dump local ` command. To ensure all data is output, -the dump frequency should correspond to the same interval of *N* -timesteps. A dump frequency of an integer multiple of *N* can be used -to regularly output a sample of the accumulated data. - ----------- - -Restart, fix_modify, run start/stop, minimize info -""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -Accumulated local data is written to :doc:`binary restart files -`. None of the :doc:`fix_modify ` options are - -relevant to this fix. No parameter of this fix can be used with the -*start/stop* keywords of the :doc:`run ` command. - -Output info -""""""""""" - -This compute calculates a local vector or local array depending on the -number of input values. The length of the vector or number of rows in -the array is the number of recorded, lost interactions. If a single -input is specified, a local vector is produced. If two or more inputs -are specified, a local array is produced where the number of columns = -the number of inputs. The vector or array can be accessed by any -command that uses local values from a compute as input. See the -:doc:`Howto output ` page for an overview of LAMMPS -output options. - -The vector or array will be floating point values that correspond to -the specified attribute. - -Restrictions -"""""""""""" - -This fix must be used in conjunction with another LAMMPS command which -generates local data and passes it to this fix. See the related -commands below for examples of such commands. - -Related commands -"""""""""""""""" - -:doc:`pair tracker ` -:doc:`bond bpm/rotational ` -:doc:`dump local ` - -Default -""""""" - -none diff --git a/doc/src/pair_tracker.rst b/doc/src/pair_tracker.rst index c3d53bcc54..d2dddd7d45 100644 --- a/doc/src/pair_tracker.rst +++ b/doc/src/pair_tracker.rst @@ -8,9 +8,10 @@ Syntax .. code-block:: LAMMPS - pair_style tracker fix_ID keyword values attribute1 attribute2 ... + pair_style tracker fix_ID N keyword values attribute1 attribute2 ... -* fix_ID = ID of associated fix store/local +* fix_ID = ID of associated internal fix to store data +* N = prepare data for output every this many timesteps * zero or more keywords may be appended * keyword = *finite* or *time/min* or *type/include* @@ -45,13 +46,12 @@ Examples .. code-block:: LAMMPS - pair_style hybrid/overlay tracker myfix id1 id2 type/include 1 * type/include 2 3,4 lj/cut 2.5 + pair_style hybrid/overlay tracker myfix 1000 id1 id2 type/include 1 * type/include 2 3,4 lj/cut 2.5 pair_coeff 1 1 tracker 2.0 - pair_style hybrid/overlay tracker myfix finite x y z time/min 100 granular + pair_style hybrid/overlay tracker myfix 1000 finite x y z time/min 100 granular pair_coeff * * tracker - fix myfix all store/local 1000 3 dump 1 all local 1000 dump.local f_myfix[1] f_myfix[2] f_myfix[3] dump_modify 1 write_header no @@ -59,18 +59,14 @@ Description """"""""""" Style *tracker* monitors information about pairwise interactions. It -does not calculate any forces on atoms. :doc:`Pair hybrid/overlay +does not calculate any forces on atoms. :doc:`Pair hybrid/overlay ` can be used to combine this pair style with any other -pair style, as shown in the examples above. Style *tracker* must also -be used in conjunction with the :doc:`fix store/local -` command which stores the pairise information so it -can be accessed as local data by other LAMMPS commands, e.g. by the -:doc:`dump local ` command for output. - +pair style, as shown in the examples above. At each timestep, if two neighboring atoms move beyond the interaction -cutoff, pairwise data is processed and transferred to the associated -instance of :doc:`fix store/local `. Additional +cutoff, pairwise data is processed and transferred to an internal fix +labeled *fix_ID*. This allows the local data to be accessed by other +LAMMPS commands. Additional filters can be applied using the *time/min* or *type/include* keywords described below. Note that this is the interaction cutoff defined by this pair style, not the short-range cutoff defined by the pair style @@ -78,13 +74,23 @@ that is calculating forces on atoms. Following any optional keyword/value arguments, a list of one or more attributes is specified. These include the IDs of the two atoms in -the pair. The other attributes for the pair of atoms are for the +the pair. The other attributes for the pair of atoms are the duration of time they were "interacting" or at the point in time they started or stopped interacting. In this context, "interacting" means the time window during which the two atoms were closer than the interaction cutoff distance. The attributes for time/* refer to timesteps. +Data is continuously accumulated by the internal fix over intervals of *N* +timesteps. At the end of each interval, all of the saved accumulated +data is deleted to make room for new data. Individual datum may +therefore persist anywhere between *1* to *N* timesteps depending on +when they are saved. This data can be accessed using the *fix_ID* and a +:doc:`dump local ` command. To ensure all data is output, +the dump frequency should correspond to the same interval of *N* +timesteps. A dump frequency of an integer multiple of *N* can be used +to regularly output a sample of the accumulated data. + ---------- The following optional keywords may be used. @@ -147,6 +153,22 @@ specified in an input script that reads a restart file. The :doc:`pair_modify ` shift, table, and tail options are not relevant for this pair style. +The accumulated data is not written to restart files and should be +output before a restart file is written to avoid missing data. + +The internal fix calculates a local vector or local array depending on the +number of input values. The length of the vector or number of rows in +the array is the number of recorded, lost interactions. If a single +input is specified, a local vector is produced. If two or more inputs +are specified, a local array is produced where the number of columns = +the number of inputs. The vector or array can be accessed by any +command that uses local values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS +output options. + +The vector or array will be floating point values that correspond to +the specified attribute. + ---------- Restrictions @@ -165,8 +187,6 @@ that extend beyond the contact (e.g. JKR and DMT). Related commands """""""""""""""" -:doc:`fix store_local ` - Default """"""" diff --git a/examples/bpm/impact/in.bpm.impact.rotational b/examples/bpm/impact/in.bpm.impact.rotational index 34443fca6f..0b3bcbe0a2 100644 --- a/examples/bpm/impact/in.bpm.impact.rotational +++ b/examples/bpm/impact/in.bpm.impact.rotational @@ -24,7 +24,6 @@ pair_style gran/hooke/history 1.0 NULL 0.5 NULL 0.1 1 pair_coeff 1 1 fix 1 all nve/sphere/bpm -fix 2 all store/local 100 3 create_bonds many plate plate 1 0.0 1.5 create_bonds many projectile projectile 2 0.0 1.5 @@ -32,7 +31,7 @@ create_bonds many projectile projectile 2 0.0 1.5 neighbor 0.3 bin special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 -bond_style bpm/rotational store/local 2 time id1 id2 +bond_style bpm/rotational store/local brkbond 100 time id1 id2 bond_coeff 1 1.0 0.2 0.02 0.02 0.05 0.01 0.01 0.01 0.1 0.02 0.002 0.002 bond_coeff 2 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.02 0.002 0.002 @@ -46,7 +45,7 @@ thermo 100 thermo_modify lost ignore lost/bond ignore #dump 1 all custom 100 atomDump id radius x y z c_nbond -dump 2 all local 100 brokenDump f_2[1] f_2[2] f_2[3] +dump 2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3] dump_modify 2 header no run 7500 diff --git a/examples/bpm/impact/in.bpm.impact.spring b/examples/bpm/impact/in.bpm.impact.spring index 60822cde01..7c5c56841b 100644 --- a/examples/bpm/impact/in.bpm.impact.spring +++ b/examples/bpm/impact/in.bpm.impact.spring @@ -26,7 +26,6 @@ pair_style bpm/spring pair_coeff 1 1 1.0 1.0 1.0 fix 1 all nve -fix 2 all store/local 100 3 create_bonds many plate plate 1 0.0 1.5 create_bonds many projectile projectile 2 0.0 1.5 @@ -34,7 +33,7 @@ create_bonds many projectile projectile 2 0.0 1.5 neighbor 0.3 bin special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 -bond_style bpm/spring store/local 2 time id1 id2 +bond_style bpm/spring store/local brkbond 100 time id1 id2 bond_coeff 1 1.0 0.04 1.0 bond_coeff 2 1.0 0.20 1.0 @@ -48,7 +47,7 @@ thermo 100 thermo_modify lost ignore lost/bond ignore #dump 1 all custom 100 atomDump id x y z c_nbond -dump 2 all local 100 brokenDump f_2[1] f_2[2] f_2[3] +dump 2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3] dump_modify 2 header no run 7500 diff --git a/examples/bpm/impact/log.27Oct2021.impact.rotational.g++.4 b/examples/bpm/impact/log.27Oct2021.impact.rotational.g++.4 new file mode 100644 index 0000000000..bb7b526ed9 --- /dev/null +++ b/examples/bpm/impact/log.27Oct2021.impact.rotational.g++.4 @@ -0,0 +1,217 @@ +LAMMPS (27 Oct 2021) +units lj +dimension 3 +boundary f f f +atom_style sphere/bpm +special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0 +newton on off +comm_modify vel yes cutoff 2.6 +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block -25 15 -22 22 -22 22 +create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50 +Created orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823) + 1 by 2 by 2 MPI processor grid + +region disk cylinder x 0.0 0.0 20.0 -0.5 0.5 +create_atoms 1 region disk +Created 7529 atoms + using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823) + create_atoms CPU = 0.006 seconds +group plate region disk +7529 atoms in group plate + +region ball sphere 8.0 0.0 0.0 6.0 +create_atoms 1 region ball +Created 3589 atoms + using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823) + create_atoms CPU = 0.001 seconds +group projectile region ball +3589 atoms in group projectile + +displace_atoms all random 0.1 0.1 0.1 134598738 +Displacing atoms ... + +neighbor 1.0 bin +pair_style gran/hooke/history 1.0 NULL 0.5 NULL 0.1 1 +pair_coeff 1 1 + +fix 1 all nve/sphere/bpm + +create_bonds many plate plate 1 0.0 1.5 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 64 70 70 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair gran/hooke/history, perpetual + attributes: half, newton on, size, history + pair build: half/size/bin/newton + stencil: half/bin/3d + bin: standard +Added 38559 bonds, new total = 38559 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 15 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.002 seconds +create_bonds many projectile projectile 2 0.0 1.5 +WARNING: Bonds are defined but no bond style is set (../force.cpp:191) +WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:193) +Added 21869 bonds, new total = 60428 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 16 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.002 seconds + +neighbor 0.3 bin +special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 + +bond_style bpm/rotational store/local brkbond 100 time id1 id2 +bond_coeff 1 1.0 0.2 0.02 0.02 0.05 0.01 0.01 0.01 0.1 0.02 0.002 0.002 +bond_coeff 2 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.02 0.002 0.002 + +velocity projectile set -0.05 0.0 0.0 +compute nbond all nbond/atom +compute tbond all reduce sum c_nbond + +timestep 0.05 +thermo_style custom step ke pe pxx pyy pzz c_tbond +thermo 100 +thermo_modify lost ignore lost/bond ignore +#dump 1 all custom 100 atomDump id radius x y z c_nbond + +dump 2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3] +dump_modify 2 header no + +run 7500 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 2.6 + binsize = 0.65, bins = 98 108 108 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hooke/history, perpetual + attributes: half, newton on, size, history + pair build: half/size/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.35 Mbytes +Step KinEng PotEng Pxx Pyy Pzz c_tbond + 0 0.00053238861 0 3.8217307e-05 0 0 10.8703 + 100 0.00053238861 0 3.8217307e-05 2.0196245e-19 2.0291801e-19 10.8703 + 200 0.00053238861 0 3.8217307e-05 3.0246341e-19 2.9178664e-19 10.8703 + 300 0.00053238861 0 3.8217307e-05 3.3428362e-19 3.2669661e-19 10.8703 + 400 0.00053238861 0 3.8217307e-05 3.5002919e-19 3.3516777e-19 10.8703 + 500 0.00053102278 0 3.8469829e-05 7.3311547e-08 1.4473347e-07 10.8703 + 600 0.00051549609 0 4.0342929e-05 3.87734e-07 4.9640786e-07 10.868322 + 700 0.00050121532 0 3.8778736e-05 4.6411496e-07 4.3149467e-07 10.850333 + 800 0.00049869661 0 3.6779398e-05 4.748259e-07 3.5191586e-07 10.803202 + 900 0.00049580923 0 3.5608764e-05 9.3667316e-07 5.0139078e-07 10.737363 + 1000 0.00049478796 0 3.5573518e-05 7.9599489e-07 6.7732416e-07 10.683396 + 1100 0.00048712204 0 3.5843955e-05 1.1345563e-06 1.4066243e-06 10.662169 + 1200 0.00048265244 0 3.5288538e-05 1.7434542e-06 1.6555952e-06 10.642921 + 1300 0.00047982046 0 3.4929699e-05 1.5116612e-06 1.1824842e-06 10.62925 + 1400 0.00048024672 0 3.4696478e-05 1.0219046e-06 9.6017582e-07 10.619716 + 1500 0.0004721757 0 3.4671814e-05 1.7623303e-06 1.6904391e-06 10.608023 + 1600 0.00045691175 0 3.3618706e-05 2.0127313e-06 2.2294075e-06 10.599208 + 1700 0.00044846472 0 3.2628068e-05 2.1732651e-06 2.6125725e-06 10.586796 + 1800 0.00044916668 0 3.2074126e-05 1.713271e-06 2.2306226e-06 10.562691 + 1900 0.00044434475 0 3.1841489e-05 1.4069412e-06 1.6739368e-06 10.540025 + 2000 0.00044011236 0 3.1535369e-05 1.8850064e-06 1.966093e-06 10.508365 + 2100 0.00043343658 0 3.1327313e-05 1.7877497e-06 1.9031224e-06 10.466271 + 2200 0.00043076716 0 3.1141775e-05 2.260934e-06 1.7405179e-06 10.428135 + 2300 0.0004252247 0 3.065038e-05 1.8685672e-06 1.6444209e-06 10.398993 + 2400 0.00042502327 0 3.0356508e-05 1.8748934e-06 1.3329686e-06 10.380644 + 2500 0.00042142831 0 3.0164965e-05 2.1119049e-06 1.7118338e-06 10.366433 + 2600 0.00042131885 0 3.0065244e-05 1.6092748e-06 1.5373156e-06 10.35456 + 2700 0.00042303607 0 3.0011813e-05 1.7496254e-06 1.77836e-06 10.327937 + 2800 0.00042148119 0 2.9849777e-05 1.5035087e-06 1.5374543e-06 10.314085 + 2900 0.00042092112 0 2.9766439e-05 1.2512363e-06 1.417453e-06 10.302572 + 3000 0.00042298628 0 2.985456e-05 1.030367e-06 1.2706193e-06 10.297536 + 3100 0.00042098731 0 2.9773119e-05 1.1020439e-06 1.3236711e-06 10.293938 + 3200 0.00042190155 0 2.975807e-05 1.0825659e-06 1.207615e-06 10.2907 + 3300 0.00041840008 0 2.9573071e-05 1.0027126e-06 1.0591685e-06 10.286562 + 3400 0.00041726315 0 2.9629012e-05 1.3206781e-06 1.0694496e-06 10.280986 + 3500 0.00041553548 0 2.9393577e-05 1.4604125e-06 1.2547784e-06 10.27361 + 3600 0.00041551693 0 2.9122892e-05 1.0944373e-06 9.6499513e-07 10.271632 + 3700 0.00041351569 0 2.8943889e-05 9.6203862e-07 8.3123719e-07 10.270192 + 3800 0.00041419735 0 2.9031969e-05 1.1893061e-06 7.9832166e-07 10.267494 + 3900 0.0004142108 0 2.8912904e-05 1.0049279e-06 9.0628823e-07 10.255442 + 4000 0.00041253668 0 2.8794779e-05 8.3301821e-07 8.2348634e-07 10.250045 + 4100 0.00041245029 0 2.8626953e-05 1.0440229e-06 9.7296445e-07 10.239971 + 4200 0.00041239868 0 2.8576872e-05 8.5677759e-07 9.4929241e-07 10.235114 + 4300 0.0004105539 0 2.845078e-05 7.9007545e-07 9.4314698e-07 10.227559 + 4400 0.00041038071 0 2.8447842e-05 8.3506095e-07 9.403948e-07 10.220363 + 4500 0.0004094738 0 2.8385536e-05 7.4474323e-07 8.9167115e-07 10.214247 + 4600 0.00040931891 0 2.8293128e-05 6.9842277e-07 8.7986292e-07 10.211189 + 4700 0.00040935826 0 2.832743e-05 7.7312621e-07 8.6571149e-07 10.208491 + 4800 0.00040894424 0 2.8290022e-05 7.560957e-07 7.8478084e-07 10.202195 + 4900 0.00040771373 0 2.8211024e-05 8.8835691e-07 7.6981867e-07 10.196816 + 5000 0.0004075835 0 2.8242057e-05 7.9265659e-07 8.5594679e-07 10.18854 + 5100 0.00040629886 0 2.8147996e-05 8.29922e-07 8.2991198e-07 10.186938 + 5200 0.00040615587 0 2.8075206e-05 7.9676977e-07 8.3313535e-07 10.183699 + 5300 0.00040623905 0 2.8061445e-05 8.5454501e-07 8.3464967e-07 10.18154 + 5400 0.00040639649 0 2.8095492e-05 9.219289e-07 8.8970884e-07 10.180281 + 5500 0.00040632069 0 2.8146737e-05 9.5125536e-07 9.2967258e-07 10.179741 + 5600 0.00040615846 0 2.8095814e-05 9.4628277e-07 9.4475909e-07 10.179201 + 5700 0.00040661759 0 2.8056252e-05 9.1418005e-07 9.3869835e-07 10.177942 + 5800 0.00040636342 0 2.7980285e-05 8.7191961e-07 9.4296893e-07 10.177042 + 5900 0.00040517906 0 2.7876934e-05 8.3277579e-07 9.2807515e-07 10.178694 + 6000 0.00040392762 0 2.7828073e-05 8.3950266e-07 9.4521092e-07 10.180166 + 6100 0.00040367162 0 2.7800472e-05 8.720166e-07 1.0332147e-06 10.179806 + 6200 0.00040335119 0 2.7762148e-05 8.5284463e-07 9.3150721e-07 10.179086 + 6300 0.00040340642 0 2.7769051e-05 8.3428098e-07 8.7041896e-07 10.178546 + 6400 0.0004030719 0 2.7741943e-05 7.952126e-07 8.3664709e-07 10.179282 + 6500 0.00040347682 0 2.7744595e-05 7.8058438e-07 8.4639064e-07 10.178382 + 6600 0.00040257759 0 2.7667961e-05 7.8150592e-07 8.5501519e-07 10.179298 + 6700 0.00040217981 0 2.7649415e-05 8.1293625e-07 9.4727792e-07 10.178938 + 6800 0.00040191405 0 2.7693195e-05 8.0894279e-07 1.1604089e-06 10.178938 + 6900 0.00040208358 0 2.7773245e-05 7.9264674e-07 1.1927033e-06 10.178758 + 7000 0.00040239724 0 2.782978e-05 8.330894e-07 1.2084905e-06 10.178758 + 7100 0.00040269303 0 2.7728862e-05 8.1375466e-07 1.0779344e-06 10.178758 + 7200 0.00040227155 0 2.7654709e-05 8.3101678e-07 9.7757461e-07 10.17969 + 7300 0.00040115701 0 2.7604211e-05 8.07161e-07 9.4401828e-07 10.181376 + 7400 0.00039998681 0 2.7528309e-05 7.8970732e-07 9.3464728e-07 10.182703 + 7500 0.00039916281 0 2.7432547e-05 7.9446882e-07 8.9887681e-07 10.182949 +Loop time of 34.6948 on 4 procs for 7500 steps with 11096 atoms + +Performance: 933857.672 tau/day, 216.171 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 | 0.32481 | 0.33445 | 0.34816 | 1.6 | 0.96 +Bond | 26.728 | 28.076 | 29.753 | 23.9 | 80.92 +Neigh | 0.68094 | 0.72261 | 0.7747 | 4.8 | 2.08 +Comm | 1.5266 | 3.3654 | 4.8309 | 75.3 | 9.70 +Output | 0.018332 | 0.018804 | 0.019756 | 0.4 | 0.05 +Modify | 1.9305 | 2.0147 | 2.1302 | 6.0 | 5.81 +Other | | 0.1631 | | | 0.47 + +Nlocal: 2774.00 ave 2898 max 2701 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 1165.25 ave 1208 max 1142 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Neighs: 11425.0 ave 12539 max 10556 min +Histogram: 1 0 1 0 1 0 0 0 0 1 + +Total # of neighbors = 45700 +Ave neighs/atom = 4.1186013 +Ave special neighs/atom = 10.184841 +Neighbor list builds = 451 +Dangerous builds = 0 +Total wall time: 0:00:35 diff --git a/examples/bpm/impact/log.27Oct2021.impact.spring.g++.4 b/examples/bpm/impact/log.27Oct2021.impact.spring.g++.4 new file mode 100644 index 0000000000..4aae247314 --- /dev/null +++ b/examples/bpm/impact/log.27Oct2021.impact.spring.g++.4 @@ -0,0 +1,219 @@ +LAMMPS (27 Oct 2021) +units lj +dimension 3 +boundary f f f +atom_style bond +special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0 +newton on off +comm_modify vel yes cutoff 2.6 +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block -25 15 -22 22 -22 22 +create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50 +Created orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823) + 1 by 2 by 2 MPI processor grid + +region disk cylinder x 0.0 0.0 20.0 -0.5 0.5 +create_atoms 1 region disk +Created 7529 atoms + using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823) + create_atoms CPU = 0.002 seconds +group plate region disk +7529 atoms in group plate + +region ball sphere 8.0 0.0 0.0 6.0 +create_atoms 1 region ball +Created 3589 atoms + using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823) + create_atoms CPU = 0.001 seconds +group projectile region ball +3589 atoms in group projectile + +displace_atoms all random 0.1 0.1 0.1 134598738 +Displacing atoms ... + +mass 1 1.0 + +neighbor 1.0 bin +pair_style bpm/spring +pair_coeff 1 1 1.0 1.0 1.0 + +fix 1 all nve + +create_bonds many plate plate 1 0.0 1.5 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 64 70 70 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 38559 bonds, new total = 38559 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 15 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.002 seconds +create_bonds many projectile projectile 2 0.0 1.5 +WARNING: Bonds are defined but no bond style is set (../force.cpp:191) +WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:193) +Added 21869 bonds, new total = 60428 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 16 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.002 seconds + +neighbor 0.3 bin +special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 + +bond_style bpm/spring store/local brkbond 100 time id1 id2 +bond_coeff 1 1.0 0.04 1.0 +bond_coeff 2 1.0 0.20 1.0 + +velocity projectile set -0.05 0.0 0.0 +compute nbond all nbond/atom +compute tbond all reduce sum c_nbond + +timestep 0.1 +thermo_style custom step ke pe pxx pyy pzz c_tbond +thermo 100 +thermo_modify lost ignore lost/bond ignore +#dump 1 all custom 100 atomDump id x y z c_nbond + +dump 2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3] +dump_modify 2 header no + +run 7500 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 2.6 + binsize = 0.65, bins = 98 108 108 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 17.74 | 17.74 | 17.74 Mbytes +Step KinEng PotEng Pxx Pyy Pzz c_tbond + 0 0.0010167873 0 7.298968e-05 0 0 10.8703 + 100 0.0010167873 0 7.298968e-05 -8.7429897e-20 -8.8470837e-20 10.8703 + 200 0.0010167873 0 7.298968e-05 -7.2809565e-20 -8.0915788e-20 10.8703 + 300 0.0009951439 0 9.9273671e-05 8.1569216e-06 8.0922512e-06 10.868142 + 400 0.00095142792 0 0.00012669557 -1.3413721e-05 -1.4800745e-05 10.849793 + 500 0.00092272662 0 8.1708784e-05 -9.7488701e-06 -1.3603634e-05 10.819752 + 600 0.00088967612 0 6.2587266e-05 -5.1954127e-06 -6.781587e-06 10.797985 + 700 0.00086070919 0 8.8529902e-05 -9.9431205e-06 -7.9905211e-06 10.776579 + 800 0.00083543943 0 7.5920357e-05 3.6381024e-07 3.7747551e-06 10.759309 + 900 0.00081190799 0 6.3678219e-05 5.4158243e-06 1.2751247e-05 10.744199 + 1000 0.00078828988 0 7.3079869e-05 -6.6410613e-06 -1.198683e-06 10.728368 + 1100 0.00075664718 0 6.2976995e-05 -4.7863299e-06 -3.9814556e-06 10.711819 + 1200 0.00072472205 0 4.9680233e-05 9.3093553e-06 4.4426393e-06 10.69401 + 1300 0.00070176532 0 5.4048176e-05 1.3051954e-05 7.5448558e-06 10.671164 + 1400 0.00068599319 0 5.4062404e-05 9.9930199e-06 1.0353154e-05 10.650117 + 1500 0.0006786164 0 4.5038593e-05 8.067571e-06 9.8825461e-06 10.636266 + 1600 0.00067466823 0 4.6733251e-05 9.8595584e-06 1.1551081e-05 10.621335 + 1700 0.00066847126 0 5.1472453e-05 2.1569974e-07 6.0070599e-06 10.6127 + 1800 0.00065711827 0 5.0355189e-05 -8.030203e-06 -3.1395588e-06 10.599568 + 1900 0.00063882539 0 4.7146888e-05 -2.0596242e-05 -1.6494542e-05 10.581939 + 2000 0.00061717894 0 4.6698781e-05 -2.5473048e-05 -2.7703615e-05 10.567188 + 2100 0.00059261327 0 3.7701055e-05 -2.4637803e-05 -3.3919162e-05 10.552617 + 2200 0.00056527158 0 3.2239421e-05 -1.8786685e-05 -2.4202734e-05 10.538406 + 2300 0.00054054919 0 2.7410334e-05 -6.701111e-06 -7.4354974e-06 10.520777 + 2400 0.00051820065 0 2.2997206e-05 1.5623767e-05 1.8687824e-05 10.501889 + 2500 0.00049647925 0 1.746693e-05 2.8814144e-05 3.5569425e-05 10.487498 + 2600 0.00047837258 0 1.4127067e-05 3.4245611e-05 4.0208577e-05 10.472387 + 2700 0.00046626924 0 1.3714876e-05 3.7922196e-05 4.1550346e-05 10.456377 + 2800 0.0004560167 0 1.5260976e-05 3.5632577e-05 3.7885738e-05 10.440007 + 2900 0.00045331059 0 1.5194832e-05 3.1036124e-05 2.8633755e-05 10.427955 + 3000 0.00045227799 0 1.4877378e-05 1.9327028e-05 2.1189487e-05 10.414283 + 3100 0.00044866178 0 2.0424612e-05 -2.7242288e-06 7.7121438e-06 10.40349 + 3200 0.00044336453 0 2.3276121e-05 -1.979069e-05 -4.2311089e-06 10.395575 + 3300 0.00043526526 0 2.3338132e-05 -2.834945e-05 -1.7302033e-05 10.389998 + 3400 0.00042817758 0 2.4374527e-05 -2.9870076e-05 -3.0623264e-05 10.382803 + 3500 0.00042182658 0 2.6120627e-05 -2.9449521e-05 -3.787776e-05 10.378126 + 3600 0.00041794291 0 2.4736957e-05 -2.4098172e-05 -3.0529166e-05 10.373628 + 3700 0.0004156005 0 2.7543305e-05 -1.2431749e-05 -1.8626096e-05 10.37075 + 3800 0.0004141461 0 2.4630482e-05 -6.345489e-06 -1.7375803e-05 10.368771 + 3900 0.00041328832 0 2.2220142e-05 4.1471034e-07 -1.3339476e-05 10.366972 + 4000 0.00041121725 0 2.3491321e-05 1.1284551e-05 -5.8651834e-06 10.364634 + 4100 0.00040761876 0 2.6688248e-05 1.9721625e-05 3.7536871e-06 10.362655 + 4200 0.00040301362 0 2.7601916e-05 1.9212118e-05 9.7175996e-06 10.359417 + 4300 0.00040001545 0 2.7243769e-05 1.6889359e-05 1.1857147e-05 10.3551 + 4400 0.00039654521 0 2.561083e-05 1.3863551e-05 1.0593597e-05 10.351142 + 4500 0.00039435924 0 2.4366458e-05 1.2545563e-05 1.1323962e-05 10.348804 + 4600 0.00039250006 0 2.3719127e-05 1.1015167e-05 8.5964046e-06 10.348444 + 4700 0.00039145496 0 2.2943915e-05 8.7824224e-06 5.0397129e-06 10.346825 + 4800 0.00039105331 0 2.4005757e-05 7.5899773e-06 9.033741e-07 10.344846 + 4900 0.0003898798 0 2.3819433e-05 4.9673894e-06 -2.3466459e-06 10.343587 + 5000 0.00038747508 0 2.3605028e-05 -1.1717437e-06 -6.1096657e-06 10.343047 + 5100 0.00038549022 0 2.3453798e-05 -9.9256693e-06 -9.3584148e-06 10.341788 + 5200 0.00038283936 0 2.5243567e-05 -1.5877598e-05 -9.9474447e-06 10.340169 + 5300 0.00038140888 0 2.5522223e-05 -1.9331435e-05 -1.1067039e-05 10.33873 + 5400 0.00037916674 0 2.5181488e-05 -2.1581255e-05 -1.1252641e-05 10.336931 + 5500 0.00037782932 0 2.691805e-05 -1.5768241e-05 -5.6704695e-06 10.334952 + 5600 0.00037628832 0 2.5851445e-05 -1.4239811e-05 -1.9122536e-06 10.333153 + 5700 0.00037451913 0 2.4758416e-05 -1.3252284e-05 -1.9222041e-06 10.331714 + 5800 0.00037328662 0 2.2507032e-05 -9.6704092e-06 -7.5470215e-06 10.330095 + 5900 0.00037253111 0 2.3303086e-05 -4.2828034e-06 -7.888056e-06 10.328476 + 6000 0.00037171133 0 2.4042456e-05 -4.7684985e-06 -6.5164336e-06 10.327397 + 6100 0.00036986726 0 2.4938695e-05 -4.8738316e-06 -4.5380007e-06 10.327037 + 6200 0.0003675822 0 2.3322229e-05 -4.6333093e-06 -5.7086464e-06 10.327037 + 6300 0.00036552389 0 2.1435354e-05 -4.8971566e-06 -3.5935426e-06 10.327037 + 6400 0.00036488091 0 2.0813994e-05 -3.8333319e-06 -3.6595059e-06 10.327037 + 6500 0.00036447973 0 2.2241876e-05 8.7797361e-08 -4.141203e-06 10.327037 + 6600 0.00036383343 0 2.269485e-05 4.9364593e-06 1.3062133e-06 10.326677 + 6700 0.00036305076 0 2.1838759e-05 6.4587048e-06 4.7758772e-06 10.326318 + 6800 0.00036226601 0 2.2916622e-05 6.044926e-06 5.0291597e-06 10.325598 + 6900 0.00036175279 0 2.2691667e-05 6.9998847e-06 5.8988637e-06 10.324699 + 7000 0.00036143633 0 2.1725813e-05 8.1268152e-06 5.0390503e-06 10.324519 + 7100 0.0003610248 0 2.1799675e-05 8.65795e-06 3.1360368e-06 10.323439 + 7200 0.00036086259 0 2.2198029e-05 5.1764734e-06 5.4798783e-07 10.32308 + 7300 0.00036099757 0 2.4160496e-05 1.0310325e-06 -5.115075e-07 10.32254 + 7400 0.00036129334 0 2.5325018e-05 -9.4918158e-07 -1.7064957e-06 10.32218 + 7500 0.00036136655 0 2.3513198e-05 -3.8618451e-06 -4.4344772e-06 10.321281 +Loop time of 5.76963 on 4 procs for 7500 steps with 11118 atoms + +Performance: 11231223.476 tau/day, 1299.910 timesteps/s +96.3% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.29183 | 0.31143 | 0.32961 | 2.4 | 5.40 +Bond | 2.76 | 2.9181 | 3.0698 | 7.2 | 50.58 +Neigh | 0.6247 | 0.6775 | 0.71319 | 4.5 | 11.74 +Comm | 0.76389 | 0.98813 | 1.2487 | 19.2 | 17.13 +Output | 0.1312 | 0.13162 | 0.13257 | 0.2 | 2.28 +Modify | 0.60526 | 0.63574 | 0.66339 | 2.6 | 11.02 +Other | | 0.1071 | | | 1.86 + +Nlocal: 2779.50 ave 2862 max 2686 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Nghost: 1183.25 ave 1220 max 1134 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Neighs: 11828.8 ave 12387 max 11053 min +Histogram: 1 0 0 0 1 0 0 0 1 1 + +Total # of neighbors = 47315 +Ave neighs/atom = 4.2557115 +Ave special neighs/atom = 10.321461 +Neighbor list builds = 421 +Dangerous builds = 11 +Total wall time: 0:00:05 diff --git a/examples/bpm/impact/log.30Jul2021.impact_rotational.g++1.4 b/examples/bpm/impact/log.30Jul2021.impact_rotational.g++1.4 deleted file mode 100644 index b81abac877..0000000000 --- a/examples/bpm/impact/log.30Jul2021.impact_rotational.g++1.4 +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS (30 Jul 2021) -units lj -dimension 3 -boundary f f f -atom_style sphere/bpm -special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0 -newton on off -comm_modify vel yes cutoff 2.6 -lattice fcc 1.0 -Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 -region box block -25 15 -22 22 -22 22 -create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50 -Created orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823) - 1 by 1 by 1 MPI processor grid - -region disk cylinder x 0.0 0.0 20.0 -0.5 0.5 -create_atoms 1 region disk -Created 7529 atoms - using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823) - create_atoms CPU = 0.004 seconds -group plate region disk -7529 atoms in group plate - -region ball sphere 8.0 0.0 0.0 6.0 -create_atoms 1 region ball -Created 3589 atoms - using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823) - create_atoms CPU = 0.002 seconds -group projectile region ball -3589 atoms in group projectile - -displace_atoms all random 0.1 0.1 0.1 134598738 -Displacing atoms ... - -neighbor 1.0 bin -pair_style gran/hooke/history 1.0 NULL 0.5 NULL 0.1 1 -bond_style bpm/rotational store/local 2 time id1 id2 -pair_coeff 1 1 -bond_coeff 1 1.0 0.2 0.02 0.02 0.05 0.01 0.01 0.01 0.1 0.02 0.002 0.002 -bond_coeff 2 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.02 0.002 0.002 - -fix 1 all nve/sphere/bpm -fix 2 all store/local 100 3 -fix 3 all update/special/bonds - -create_bonds many plate plate 1 0.0 1.5 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2.6 - binsize = 1, bins = 64 70 70 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) command create_bonds, occasional - attributes: full, newton on - pair build: full/bin - stencil: full/bin/3d - bin: standard - (2) pair gran/hooke/history, perpetual - attributes: half, newton on, size, history - pair build: half/size/bin/newton - stencil: half/bin/3d - bin: standard -Added 38559 bonds, new total = 38559 -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 1 1 - special bond factors coul: 0 1 1 - 15 = max # of 1-2 neighbors - 101 = max # of special neighbors - special bonds CPU = 0.007 seconds -create_bonds many projectile projectile 2 0.0 1.5 -Added 21869 bonds, new total = 60428 -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 1 1 - special bond factors coul: 0 1 1 - 16 = max # of 1-2 neighbors - 101 = max # of special neighbors - special bonds CPU = 0.010 seconds - -neighbor 0.3 bin -special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 - -velocity projectile set -0.05 0.0 0.0 -compute nbond all nbond/atom -compute tbond all reduce sum c_nbond - -timestep 0.05 -thermo_style custom step ke pe pxx pyy pzz c_tbond -thermo 100 -thermo_modify lost ignore lost/bond ignore -#dump 1 all custom 100 atomDump id radius x y z c_nbond - -dump 2 all local 100 brokenDump f_2[1] f_2[2] f_2[3] -dump_modify 2 header no - -run 7500 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.3 - ghost atom cutoff = 2.6 - binsize = 0.65, bins = 98 108 108 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair gran/hooke/history, perpetual - attributes: half, newton on, size, history - pair build: half/size/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 39.18 | 39.18 | 39.18 Mbytes -Step KinEng PotEng Pxx Pyy Pzz c_tbond - 0 0.00053238861 0 3.8217307e-05 0 0 10.8703 - 100 0.00053238861 0 3.8217307e-05 3.7024766e-13 -2.6107956e-13 10.8703 - 200 0.00053238861 0 3.8217307e-05 -4.6764996e-13 5.7734804e-13 10.8703 - 300 0.00053238861 0 3.8217308e-05 -6.6404932e-13 -1.4463201e-13 10.8703 - 400 0.00053238861 0 3.8217307e-05 -1.5842255e-13 3.2646699e-14 10.8703 - 500 0.00053102307 0 3.6857657e-05 -5.0613842e-07 -4.5464639e-07 10.8703 - 600 0.00051549565 0 1.5836226e-05 -6.6250357e-06 -7.1458399e-06 10.868322 - 700 0.00050120381 0 -1.9467767e-05 -7.7209878e-06 -1.121158e-05 10.850333 - 800 0.00049861454 0 1.5365076e-05 5.214591e-06 2.7950985e-06 10.803742 - 900 0.00049582022 0 5.7445368e-05 -2.1846154e-05 -2.3927093e-05 10.738082 - 1000 0.00049342915 0 4.9596969e-05 -8.1907786e-06 -1.3269952e-05 10.688433 - 1100 0.00048639213 0 1.0822487e-05 3.9352339e-05 4.0409565e-05 10.667026 - 1200 0.000483091 0 3.8492853e-06 2.2015581e-05 3.1490077e-05 10.646159 - 1300 0.00047987023 0 5.8429983e-05 -7.8096854e-06 3.9318833e-06 10.631229 - 1400 0.00048104927 0 4.6603937e-05 -1.2320299e-05 -1.010841e-05 10.619536 - 1500 0.00047270384 0 -1.622772e-06 1.5996657e-05 1.5652658e-05 10.606944 - 1600 0.00045720595 0 1.64434e-06 1.0627449e-05 7.2901589e-06 10.597949 - 1700 0.00044826095 0 3.3113848e-05 -3.1886382e-05 -4.1076437e-05 10.584458 - 1800 0.00044859158 0 3.8589858e-05 -3.217135e-05 -4.4394932e-05 10.554236 - 1900 0.00044410417 0 1.6071124e-06 3.469787e-06 -1.172431e-05 10.528153 - 2000 0.00043690537 0 1.8298385e-05 3.2800463e-05 2.3766026e-05 10.49955 - 2100 0.00043113053 0 5.5169319e-05 1.0337577e-05 6.8334001e-06 10.449541 - 2200 0.00042795839 0 3.3555532e-05 -7.8682107e-06 1.4501739e-06 10.40277 - 2300 0.0004240013 0 8.8868452e-06 1.8196289e-06 2.755748e-05 10.362115 - 2400 0.00042426888 0 2.3953861e-05 1.7614888e-05 4.2827512e-05 10.340529 - 2500 0.00041903776 0 5.1969184e-05 2.5725967e-05 4.2229194e-05 10.324879 - 2600 0.00042070944 0 4.0633614e-05 2.6089786e-05 3.2212886e-05 10.313006 - 2700 0.00041907255 0 1.0826647e-05 2.7725133e-05 3.3535626e-05 10.301673 - 2800 0.00041823551 0 2.7757924e-05 1.462054e-05 1.629062e-05 10.288001 - 2900 0.00041833009 0 5.016926e-05 2.1116657e-06 -9.0474367e-06 10.276129 - 3000 0.0004200714 0 2.9312093e-05 8.0995894e-06 -1.427634e-05 10.266954 - 3100 0.00041930877 0 8.2905585e-06 2.5106255e-06 -6.0475079e-06 10.259039 - 3200 0.00042002824 0 2.7415565e-05 -2.5467008e-05 -1.1758229e-05 10.249146 - 3300 0.00041772304 0 4.7010143e-05 -3.2166248e-05 -2.3740064e-05 10.245728 - 3400 0.00041567147 0 2.265559e-05 -1.4994351e-05 -1.4387458e-05 10.244828 - 3500 0.00041264993 0 9.4675076e-06 -1.2940542e-05 -2.6164909e-06 10.243929 - 3600 0.00041296772 0 3.2135436e-05 -2.3723233e-05 -1.1358132e-05 10.243029 - 3700 0.00041218299 0 4.3546104e-05 -1.6744403e-05 -2.1466737e-05 10.240871 - 3800 0.00041196427 0 2.4626877e-05 8.2428335e-06 -9.6621514e-06 10.236913 - 3900 0.00041061174 0 1.5527454e-05 1.4796165e-05 8.5041818e-06 10.229718 - 4000 0.00041008163 0 3.6758236e-05 -4.1693239e-06 -2.3638032e-07 10.221083 - 4100 0.00040807476 0 4.2903311e-05 -8.7361319e-06 -9.2843568e-06 10.211909 - 4200 0.00040749974 0 2.1764542e-05 -1.5964475e-07 1.1116464e-06 10.205972 - 4300 0.00040585168 0 1.6398189e-05 -6.2081757e-07 1.4245018e-05 10.203454 - 4400 0.00040614156 0 3.8921994e-05 -1.0816449e-05 8.8070462e-06 10.198237 - 4500 0.00040550623 0 4.1195875e-05 -4.4468565e-06 -4.5109048e-06 10.19356 - 4600 0.00040471568 0 1.9924175e-05 8.0584659e-06 2.8014197e-06 10.186904 - 4700 0.00040443998 0 2.0848233e-05 7.2219213e-06 8.5736771e-06 10.182947 - 4800 0.00040411017 0 3.8995426e-05 -3.5139599e-06 -1.7346701e-06 10.17773 - 4900 0.00040369283 0 3.8616558e-05 -3.8837458e-07 -6.5227651e-06 10.174492 - 5000 0.00040347603 0 1.957792e-05 5.3591428e-06 5.0851337e-06 10.171074 - 5100 0.00040318 0 2.0628515e-05 -6.133528e-06 8.9227218e-06 10.166217 - 5200 0.00040396442 0 3.9097282e-05 -1.3317561e-05 -2.4599499e-06 10.158842 - 5300 0.00040420662 0 3.5316538e-05 -1.4346009e-06 -5.7802302e-06 10.154704 - 5400 0.00040419432 0 1.9706975e-05 6.6651292e-06 3.0821293e-06 10.148768 - 5500 0.00040500025 0 2.2492943e-05 -8.2260426e-06 4.6721228e-06 10.14463 - 5600 0.00040447185 0 3.8628198e-05 -8.844675e-06 -6.7043678e-07 10.143191 - 5700 0.00040435949 0 3.5236357e-05 5.3512632e-06 -2.9663861e-07 10.141752 - 5800 0.00040356839 0 1.8078404e-05 7.7468465e-06 4.1618489e-06 10.141045 - 5900 0.00040255066 0 2.5803838e-05 9.5521231e-07 3.4211797e-06 10.14251 - 6000 0.00040255799 0 3.8202776e-05 -3.5222942e-06 -7.4050996e-06 10.14233 - 6100 0.00040280742 0 3.0004475e-05 2.0612828e-06 -7.0155478e-06 10.14197 - 6200 0.00040180209 0 1.8453425e-05 2.5937959e-06 6.019204e-06 10.142703 - 6300 0.00040159364 0 2.6608078e-05 -3.4326767e-06 6.5089502e-06 10.142163 - 6400 0.00039963271 0 3.7746341e-05 -1.3954533e-06 -6.6816781e-06 10.143076 - 6500 0.0003995975 0 2.7758521e-05 6.370558e-06 -8.535581e-06 10.143076 - 6600 0.00039973428 0 1.8062746e-05 6.3493548e-06 1.2970441e-06 10.143076 - 6700 0.00039987367 0 2.7872598e-05 2.9794629e-07 3.1449123e-06 10.143988 - 6800 0.00039942046 0 3.6871697e-05 4.4181241e-07 -3.7266658e-06 10.146188 - 6900 0.00039937936 0 2.73304e-05 6.4090146e-06 1.1834424e-06 10.147835 - 7000 0.00039934517 0 2.0161434e-05 5.3875016e-06 1.141564e-05 10.147835 - 7100 0.00039884824 0 3.0603701e-05 7.327098e-07 5.1369462e-06 10.148402 - 7200 0.00039774709 0 3.5965545e-05 3.6906864e-06 -5.6506465e-06 10.148969 - 7300 0.00039642146 0 2.4883695e-05 7.2866197e-06 -8.2009411e-07 10.151379 - 7400 0.00039605388 0 2.0790699e-05 2.6616664e-06 1.1522615e-05 10.152321 - 7500 0.00039471805 0 3.0911798e-05 -4.6441697e-06 5.9470361e-06 10.154748 -Loop time of 114.934 on 1 procs for 7500 steps with 11089 atoms - -Performance: 281901.613 tau/day, 65.255 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 | 1.2383 | 1.2383 | 1.2383 | 0.0 | 1.08 -Bond | 101.4 | 101.4 | 101.4 | 0.0 | 88.22 -Neigh | 2.7723 | 2.7723 | 2.7723 | 0.0 | 2.41 -Comm | 0.075342 | 0.075342 | 0.075342 | 0.0 | 0.07 -Output | 0.06732 | 0.06732 | 0.06732 | 0.0 | 0.06 -Modify | 9.1154 | 9.1154 | 9.1154 | 0.0 | 7.93 -Other | | 0.2695 | | | 0.23 - -Nlocal: 11089.0 ave 11089 max 11089 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0.00000 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 45554.0 ave 45554 max 45554 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 45554 -Ave neighs/atom = 4.1080350 -Ave special neighs/atom = 10.156101 -Neighbor list builds = 467 -Dangerous builds = 0 -Total wall time: 0:01:55 diff --git a/examples/bpm/impact/log.30Jul2021.impact_spring.g++1.4 b/examples/bpm/impact/log.30Jul2021.impact_spring.g++1.4 deleted file mode 100644 index e3df7fbdd4..0000000000 --- a/examples/bpm/impact/log.30Jul2021.impact_spring.g++1.4 +++ /dev/null @@ -1,218 +0,0 @@ -LAMMPS (30 Jul 2021) -units lj -dimension 3 -boundary f f f -atom_style bond -special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0 -newton on off -comm_modify vel yes cutoff 2.6 -lattice fcc 1.0 -Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 -region box block -25 15 -22 22 -22 22 -create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50 -Created orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823) - 1 by 1 by 1 MPI processor grid - -region disk cylinder x 0.0 0.0 20.0 -0.5 0.5 -create_atoms 1 region disk -Created 7529 atoms - using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823) - create_atoms CPU = 0.002 seconds -group plate region disk -7529 atoms in group plate - -region ball sphere 8.0 0.0 0.0 6.0 -create_atoms 1 region ball -Created 3589 atoms - using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823) - create_atoms CPU = 0.001 seconds -group projectile region ball -3589 atoms in group projectile - -displace_atoms all random 0.1 0.1 0.1 134598738 -Displacing atoms ... - -mass 1 1.0 - -neighbor 1.0 bin -pair_style bpm/spring -bond_style bpm/spring store/local 2 time id1 id2 -pair_coeff 1 1 1.0 1.0 1.0 -bond_coeff 1 1.0 0.04 1.0 -bond_coeff 2 1.0 0.20 1.0 - -fix 1 all nve -fix 2 all store/local 100 3 -fix 3 all update/special/bonds - -create_bonds many plate plate 1 0.0 1.5 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2.6 - binsize = 1, bins = 64 70 70 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) command create_bonds, occasional - attributes: full, newton on - pair build: full/bin - stencil: full/bin/3d - bin: standard - (2) pair bpm/spring, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Added 38559 bonds, new total = 38559 -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 1 1 - special bond factors coul: 0 1 1 - 15 = max # of 1-2 neighbors - 101 = max # of special neighbors - special bonds CPU = 0.004 seconds -create_bonds many projectile projectile 2 0.0 1.5 -WARNING: Communication cutoff 2.6 is shorter than a bond length based estimate of 2.799982026012842. This may lead to errors. (../comm.cpp:734) -Added 21869 bonds, new total = 60428 -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 1 1 - special bond factors coul: 0 1 1 - 16 = max # of 1-2 neighbors - 101 = max # of special neighbors - special bonds CPU = 0.005 seconds - -neighbor 0.3 bin -special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 - -velocity projectile set -0.05 0.0 0.0 -compute nbond all nbond/atom -compute tbond all reduce sum c_nbond - -timestep 0.1 -thermo_style custom step ke pe pxx pyy pzz c_tbond -thermo 100 -thermo_modify lost ignore lost/bond ignore -dump 1 all custom 100 atomDump id x y z c_nbond - -dump 2 all local 100 brokenDump f_2[1] f_2[2] f_2[3] -dump_modify 2 header no - -run 7500 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.3 - ghost atom cutoff = 2.6 - binsize = 0.65, bins = 98 108 108 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair bpm/spring, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 24.30 | 24.30 | 24.30 Mbytes -Step KinEng PotEng Pxx Pyy Pzz c_tbond - 0 0.0010167873 0 7.298968e-05 0 0 10.8703 - 100 0.0010167873 0 7.298968e-05 -8.7429897e-20 -8.8470837e-20 10.8703 - 200 0.0010167873 0 7.298968e-05 -7.2809565e-20 -8.0915788e-20 10.8703 - 300 0.00099636578 -7.0816681e-06 9.8353035e-05 8.4642384e-06 8.0469072e-06 10.867242 - 400 0.00095644407 -4.9965293e-06 0.00012441378 -1.2397227e-05 -1.4980269e-05 10.839719 - 500 0.00092977183 -3.86131e-06 7.8605818e-05 -2.7329699e-06 -7.396399e-06 10.799424 - 600 0.00089787559 -2.9680488e-06 6.335469e-05 2.1448463e-06 4.5296678e-07 10.768663 - 700 0.00087244204 -2.6549464e-06 8.7340708e-05 -4.5516627e-06 -1.8690112e-06 10.74186 - 800 0.00084695959 -3.8045185e-06 8.0745955e-05 -4.5691607e-06 -1.6326641e-06 10.715237 - 900 0.00082108378 -3.7632176e-06 6.6501438e-05 -4.9020688e-06 3.5594859e-06 10.691131 - 1000 0.00079998853 -4.8468066e-06 6.5750228e-05 -8.3521669e-06 5.2266599e-06 10.66127 - 1100 0.00077368031 -2.5220164e-06 5.8210276e-05 2.6426591e-06 4.938121e-06 10.643461 - 1200 0.00074855587 -2.9570391e-06 5.2368186e-05 1.6897526e-06 2.4286268e-06 10.622054 - 1300 0.00072611594 -3.7109651e-06 5.8006188e-05 -2.6857728e-06 -5.6178729e-06 10.595611 - 1400 0.00070923315 -4.2629754e-06 5.3503366e-05 4.7475371e-06 -7.7268696e-06 10.569347 - 1500 0.00069740085 -3.0765543e-06 4.6753588e-05 1.2633383e-05 2.5315165e-06 10.540925 - 1600 0.00068657492 -3.0455076e-06 5.1582206e-05 1.4017258e-05 8.8044278e-06 10.519338 - 1700 0.00067656011 -3.4280513e-06 5.0396015e-05 8.4547122e-06 8.0820402e-06 10.50045 - 1800 0.00066870293 -3.4484153e-06 4.815639e-05 7.5212913e-07 1.1483891e-06 10.488217 - 1900 0.00065786507 -4.2634733e-06 4.9330522e-05 -1.108344e-05 -7.4259153e-06 10.474726 - 2000 0.00064106212 -4.7031033e-06 4.552393e-05 -1.7535521e-05 -1.6263295e-05 10.453139 - 2100 0.00062134889 -3.5304279e-06 3.809727e-05 -2.2412517e-05 -2.2946813e-05 10.433891 - 2200 0.00059830887 -3.2395481e-06 3.5740566e-05 -1.796758e-05 -1.8599386e-05 10.417881 - 2300 0.00057522207 -2.9905465e-06 3.4002427e-05 -6.7236311e-06 -1.4718938e-05 10.401511 - 2400 0.00055324818 -4.519622e-06 2.8286989e-05 5.379357e-06 -2.3963109e-06 10.383342 - 2500 0.00053140276 -4.5450401e-06 2.6655404e-05 1.4698667e-05 1.5782329e-05 10.362835 - 2600 0.00051144636 -4.1683588e-06 2.4944253e-05 2.5072313e-05 2.3558987e-05 10.33837 - 2700 0.00049421672 -5.8949891e-06 2.0313469e-05 2.4375973e-05 2.3609392e-05 10.320921 - 2800 0.00047936442 -5.7929485e-06 1.8523402e-05 1.6894086e-05 2.34875e-05 10.29016 - 2900 0.00046579117 -6.7340102e-06 1.8239135e-05 1.9583159e-05 1.821014e-05 10.266954 - 3000 0.00045439794 -5.5845157e-06 1.7413232e-05 2.0937177e-05 1.0934407e-05 10.246447 - 3100 0.00044541881 -5.1519292e-06 1.6153079e-05 1.4874654e-05 4.1969429e-06 10.233495 - 3200 0.00043791644 -5.0105552e-06 2.0005341e-05 4.7318756e-06 1.4446699e-08 10.223961 - 3300 0.00043012829 -4.8924048e-06 2.275482e-05 -6.5889472e-07 2.8411666e-06 10.212448 - 3400 0.00042478693 -4.7736643e-06 1.8655218e-05 -1.0408543e-05 -2.5097213e-06 10.203814 - 3500 0.00041885602 -4.1938783e-06 1.6924096e-05 -1.6723773e-05 -1.0907364e-05 10.197158 - 3600 0.00041470126 -4.4256374e-06 2.1660002e-05 -1.2589975e-05 -8.9195821e-06 10.191042 - 3700 0.00041103162 -4.0558298e-06 2.1463315e-05 -1.1052983e-05 -1.1288374e-05 10.186185 - 3800 0.0004064031 -4.085737e-06 2.1186979e-05 -7.6827664e-06 -8.4420523e-06 10.182407 - 3900 0.00040439659 -3.8043843e-06 2.2246535e-05 -9.8091295e-06 -6.337729e-06 10.179169 - 4000 0.00040248064 -5.207414e-06 2.4991678e-05 -8.9269116e-06 -1.3269351e-06 10.175931 - 4100 0.00039984629 -3.9470913e-06 2.0638508e-05 -1.0311727e-05 -7.0570926e-07 10.171973 - 4200 0.00039748539 -4.1530392e-06 2.2201704e-05 -1.9419136e-06 3.9363863e-06 10.169995 - 4300 0.00039699527 -4.4361889e-06 2.4637559e-05 3.0466639e-06 2.6075192e-06 10.167836 - 4400 0.00039577202 -4.5243252e-06 2.3254304e-05 9.3960261e-06 7.0976687e-06 10.165138 - 4500 0.00039438637 -4.4623531e-06 2.5479152e-05 1.3111125e-05 9.1080155e-06 10.163699 - 4600 0.00039279153 -4.3667553e-06 2.4372973e-05 1.6089732e-05 8.9825485e-06 10.162439 - 4700 0.00039304328 -4.0850029e-06 2.3031657e-05 1.4377571e-05 1.0046115e-05 10.161 - 4800 0.0003930794 -4.2247499e-06 2.3528523e-05 8.7677526e-06 1.1123548e-05 10.16082 - 4900 0.00039357048 -4.0441827e-06 2.2238523e-05 7.0463814e-06 1.0318253e-05 10.160281 - 5000 0.00039305174 -4.0989874e-06 2.3082845e-05 4.7559622e-06 9.1784689e-06 10.159561 - 5100 0.00039281446 -3.9654637e-06 2.4406601e-05 6.6792841e-07 3.9479578e-06 10.158662 - 5200 0.00039266969 -3.7000839e-06 2.3342952e-05 -4.0814362e-07 -1.7091512e-07 10.157762 - 5300 0.00039179548 -3.6041015e-06 2.2308731e-05 -2.3038721e-06 -7.7478695e-06 10.156863 - 5400 0.00039126557 -3.3816417e-06 2.5032837e-05 -4.2112558e-06 -1.0544895e-05 10.155244 - 5500 0.00039013707 -3.2015334e-06 2.4333377e-05 -9.4600548e-06 -8.164991e-06 10.153985 - 5600 0.00038863118 -3.2457645e-06 2.5234836e-05 -1.3025121e-05 -4.212353e-06 10.152545 - 5700 0.00038755505 -3.1192824e-06 2.4611567e-05 -1.7034285e-05 -7.4484904e-06 10.150926 - 5800 0.00038682794 -3.159343e-06 2.4790374e-05 -2.1244353e-05 -9.5959604e-06 10.150027 - 5900 0.00038514658 -3.1365816e-06 2.4775049e-05 -2.013337e-05 -8.7609997e-06 10.147688 - 6000 0.00038273205 -3.5768746e-06 2.4513287e-05 -1.7197146e-05 -7.7627989e-06 10.14553 - 6100 0.00038118307 -3.2886293e-06 2.4104512e-05 -1.1683647e-05 -9.0156319e-06 10.144091 - 6200 0.00037877747 -3.5457022e-06 2.546258e-05 -5.3008572e-06 -1.0680602e-05 10.142292 - 6300 0.00037631131 -3.7852195e-06 2.4823247e-05 -5.9313668e-06 -8.837521e-06 10.141033 - 6400 0.00037412558 -4.1058533e-06 2.434972e-05 -5.8192486e-06 -1.9415666e-06 10.139773 - 6500 0.00037259808 -4.0091084e-06 2.4652474e-05 -4.5769183e-06 -2.9449568e-06 10.137974 - 6600 0.00037090733 -4.1292855e-06 2.4417194e-05 -4.1646449e-06 8.6273141e-07 10.134916 - 6700 0.00036992828 -4.0221056e-06 2.3588901e-05 -6.8333754e-06 -2.5804065e-07 10.133477 - 6800 0.00036883832 -4.0617393e-06 2.4407327e-05 -4.6933138e-06 5.9097433e-07 10.131319 - 6900 0.00036806181 -3.98881e-06 2.5070794e-05 -1.8839397e-06 1.8686666e-06 10.129879 - 7000 0.00036759453 -3.8395938e-06 2.499485e-05 5.8078766e-06 5.491628e-06 10.12844 - 7100 0.00036661989 -3.807276e-06 2.3841577e-05 9.8514185e-06 2.8498309e-06 10.125922 - 7200 0.0003643494 -3.8754489e-06 2.4003718e-05 6.4101669e-06 -1.0308979e-06 10.124483 - 7300 0.00036261161 -3.8682002e-06 2.345457e-05 6.5773508e-06 1.0241788e-06 10.123583 - 7400 0.00036215882 -3.8404085e-06 2.2989219e-05 1.3012853e-05 5.3465279e-06 10.122324 - 7500 0.00036219767 -3.7430511e-06 2.6189702e-05 1.3646428e-05 7.8525122e-06 10.121065 -Loop time of 17.1159 on 1 procs for 7500 steps with 11118 atoms - -Performance: 3785956.989 tau/day, 438.189 timesteps/s -97.1% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.1678 | 1.1678 | 1.1678 | 0.0 | 6.82 -Bond | 7.299 | 7.299 | 7.299 | 0.0 | 42.64 -Neigh | 3.105 | 3.105 | 3.105 | 0.0 | 18.14 -Comm | 0.049905 | 0.049905 | 0.049905 | 0.0 | 0.29 -Output | 1.4391 | 1.4391 | 1.4391 | 0.0 | 8.41 -Modify | 3.8866 | 3.8866 | 3.8866 | 0.0 | 22.71 -Other | | 0.1685 | | | 0.98 - -Nlocal: 11118.0 ave 11118 max 11118 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0.00000 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 47063.0 ave 47063 max 47063 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 47063 -Ave neighs/atom = 4.2330455 -Ave special neighs/atom = 10.121065 -Neighbor list builds = 464 -Dangerous builds = 1 -Total wall time: 0:00:17 diff --git a/examples/bpm/pour/log.27Oct2021.pour.g++.1 b/examples/bpm/pour/log.27Oct2021.pour.g++.1 new file mode 100644 index 0000000000..ea2aecd702 --- /dev/null +++ b/examples/bpm/pour/log.27Oct2021.pour.g++.1 @@ -0,0 +1,1091 @@ +LAMMPS (27 Oct 2021) +units lj +dimension 3 +boundary m m m +atom_style sphere/bpm +special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 +newton on off +comm_modify vel yes cutoff 3.3 +region box block -15 15 -15 15 0 60.0 +create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50 +Created orthogonal box = (-15.000000 -15.000000 0.0000000) to (15.000000 15.000000 60.000000) + 1 by 1 by 1 MPI processor grid + +molecule my_mol "rect.mol" +Read molecule template my_mol: + 1 molecules + 0 fragments + 63 atoms with max type 1 + 297 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region wall_cyl cylinder z 0.0 0.0 10.0 EDGE EDGE side in +region dropzone cylinder z 0.0 0.0 10.0 40.0 50.0 side in + +pair_style gran/hertz/history 1.0 NULL 0.5 NULL 0.1 1 +bond_style bpm/rotational +pair_coeff 1 1 +bond_coeff 1 1.0 0.2 0.01 0.01 2.0 0.4 0.02 0.02 0.2 0.04 0.002 0.002 + +compute nbond all nbond/atom +compute tbond all reduce sum c_nbond +compute_modify thermo_temp dynamic/dof yes + +fix 1 all wall/gran hertz/history 1.0 NULL 0.5 NULL 0.1 1 zplane 0.0 NULL +fix 2 all wall/gran/region hertz/history 1.0 NULL 0.5 NULL 0.1 1 region wall_cyl +fix 3 all gravity 1e-4 vector 0 0 -1 +fix 4 all deposit 40 0 1500 712511343 mol my_mol region dropzone near 2.0 vz -0.05 -0.05 +fix 5 all nve/sphere/bpm + +timestep 0.05 +thermo_style custom step ke pe pxx pyy pzz c_tbond +thermo 100 +#dump 1 all custom 500 atomDump id radius x y z c_nbond mol + +run 100000 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 3.3 + binsize = 0.65, bins = 47 47 93 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hertz/history, perpetual + attributes: half, newton on, size, history + pair build: half/size/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.455 | 7.455 | 7.455 Mbytes +Step KinEng PotEng Pxx Pyy Pzz c_tbond + 0 -0 0 0 0 0 0 + 100 0.0018350009 0 2.0294872e-07 1.2112294e-06 2.871091e-06 9.4285714 + 200 0.0026448827 0 7.6279587e-07 2.0778573e-06 3.3379229e-06 9.4285714 + 300 0.0037670874 0 3.9556015e-07 5.4333498e-06 2.9911029e-06 9.4285714 + 400 0.0060865434 0 1.6646599e-06 8.4961343e-06 4.0676208e-06 9.4285714 + 500 0.0074581799 0 1.6593722e-06 1.1564338e-05 4.2088772e-06 9.4285714 + 600 0.0078577632 0 1.1090617e-06 1.3870259e-05 3.3849787e-06 9.4285714 + 700 0.0075356935 0 1.1860992e-06 1.2423274e-05 3.9852176e-06 9.4285714 + 800 0.0073700733 0 1.2020231e-06 1.2772167e-05 3.2382575e-06 9.4285714 + 900 0.0075286722 0 1.1889762e-06 1.3249052e-05 3.1364682e-06 9.4285714 + 1000 0.0075662049 0 9.7821223e-07 1.3244288e-05 3.4489011e-06 9.4285714 + 1100 0.0075478247 0 2.1523741e-06 1.2154775e-05 3.3141837e-06 9.4285714 + 1200 0.0075157382 0 1.8293606e-06 1.2430238e-05 3.2847737e-06 9.4285714 + 1300 0.0075727908 0 1.8169654e-06 1.24965e-05 3.3704876e-06 9.4285714 + 1400 0.0076061393 0 3.235313e-06 1.0568101e-05 3.9516909e-06 9.4285714 + 1500 0.0075843344 0 2.8081603e-06 1.1079699e-05 3.8236112e-06 9.4285714 + 1600 0.0059669597 0 4.3734615e-06 1.6939808e-05 6.562706e-06 9.4285714 + 1700 0.0080609915 0 5.879456e-06 2.4453021e-05 7.3267921e-06 9.4285714 + 1800 0.008774447 0 5.9362465e-06 2.7360342e-05 7.6740751e-06 9.4285714 + 1900 0.0087088165 0 6.1871839e-06 2.651416e-05 7.9542363e-06 9.4285714 + 2000 0.0087013604 0 6.265003e-06 2.6273818e-05 8.0842249e-06 9.4285714 + 2100 0.0084280051 0 6.9477803e-06 2.5301892e-05 9.0531791e-06 9.4285714 + 2200 0.0083665332 0 8.2583657e-06 2.3408918e-05 8.5164662e-06 9.4285714 + 2300 0.0083481041 0 8.3655638e-06 2.2441951e-05 8.1588379e-06 9.4285714 + 2400 0.0082989206 0 7.8320098e-06 2.214764e-05 8.7594404e-06 9.4285714 + 2500 0.0083831827 0 7.2186023e-06 2.2823611e-05 9.08778e-06 9.4285714 + 2600 0.0084024229 0 7.0626722e-06 2.2893292e-05 9.2638369e-06 9.4285714 + 2700 0.0083044462 0 7.4847584e-06 2.3286575e-05 1.0147536e-05 9.4285714 + 2800 0.0073772276 0 1.0024518e-05 1.6545269e-05 1.0697191e-05 9.4285714 + 2900 0.0072858299 0 8.9107749e-06 1.4628491e-05 1.0788204e-05 9.4285714 + 3000 0.0073545918 0 8.7084385e-06 1.4498263e-05 1.1127326e-05 9.4285714 + 3100 0.0050344502 0 7.4556928e-06 1.3880959e-05 1.3917065e-05 9.4285714 + 3200 0.0046675954 0 5.8496582e-06 1.1874352e-05 1.4957017e-05 9.4285714 + 3300 0.0047886619 0 5.7824084e-06 1.161982e-05 1.6128046e-05 9.4285714 + 3400 0.00489288 0 6.1521355e-06 1.2558603e-05 1.5545005e-05 9.4285714 + 3500 0.0048680793 0 6.1955156e-06 1.3253713e-05 1.5278308e-05 9.4285714 + 3600 0.0047352707 0 7.3854257e-06 1.4018671e-05 1.5533577e-05 9.4285714 + 3700 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5.2910041e-06 5.4163556e-06 6.9400122e-06 9.4285714 + 91700 7.3559371e-07 0 5.3055219e-06 5.455723e-06 7.044799e-06 9.4285714 + 91800 7.1536716e-07 0 5.3171425e-06 5.4958276e-06 7.1764255e-06 9.4285714 + 91900 7.3505787e-07 0 5.3414305e-06 5.5291435e-06 7.3166969e-06 9.4285714 + 92000 7.4077724e-07 0 5.3814858e-06 5.5514528e-06 7.4343294e-06 9.4285714 + 92100 6.9877049e-07 0 5.4390474e-06 5.5727673e-06 7.4953117e-06 9.4285714 + 92200 6.4252681e-07 0 5.4916149e-06 5.5977627e-06 7.5227736e-06 9.4285714 + 92300 6.0110022e-07 0 5.5159103e-06 5.6313603e-06 7.5388191e-06 9.4285714 + 92400 5.816128e-07 0 5.5178607e-06 5.6647579e-06 7.5582377e-06 9.4285714 + 92500 5.9153109e-07 0 5.5092078e-06 5.6729251e-06 7.5696663e-06 9.4285714 + 92600 6.0921987e-07 0 5.4970327e-06 5.6615892e-06 7.5703268e-06 9.4285714 + 92700 6.1337515e-07 0 5.4942697e-06 5.6345531e-06 7.5559086e-06 9.4285714 + 92800 6.1327785e-07 0 5.4807468e-06 5.6009851e-06 7.5214857e-06 9.4285714 + 92900 6.1792714e-07 0 5.4554294e-06 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6.8335849e-06 9.4285714 + 94300 6.851547e-07 0 5.4386351e-06 5.4819488e-06 6.785467e-06 9.4285714 + 94400 6.9002759e-07 0 5.4150889e-06 5.4560812e-06 6.7512517e-06 9.4285714 + 94500 6.8881467e-07 0 5.389498e-06 5.4249696e-06 6.7436813e-06 9.4285714 + 94600 6.8216567e-07 0 5.3596704e-06 5.3960045e-06 6.752434e-06 9.4285714 + 94700 6.9513876e-07 0 5.3315299e-06 5.3638382e-06 6.7588407e-06 9.4285714 + 94800 7.3117806e-07 0 5.319681e-06 5.3328405e-06 6.7594305e-06 9.4285714 + 94900 7.4630526e-07 0 5.3264247e-06 5.3065749e-06 6.7584815e-06 9.4285714 + 95000 7.052145e-07 0 5.336904e-06 5.2901046e-06 6.7591167e-06 9.4285714 + 95100 6.5300672e-07 0 5.3431675e-06 5.3055137e-06 6.7707775e-06 9.4285714 + 95200 6.2832435e-07 0 5.343062e-06 5.3566209e-06 6.8007939e-06 9.4285714 + 95300 5.8243636e-07 0 5.3391408e-06 5.411327e-06 6.8329844e-06 9.4285714 + 95400 5.3752036e-07 0 5.3329329e-06 5.4406204e-06 6.8573377e-06 9.4285714 + 95500 5.5141526e-07 0 5.3399002e-06 5.4506865e-06 6.8841697e-06 9.4285714 + 95600 5.9422206e-07 0 5.3628211e-06 5.4526761e-06 6.9223868e-06 9.4285714 + 95700 6.0502271e-07 0 5.3849027e-06 5.448663e-06 6.9748494e-06 9.4285714 + 95800 5.9633233e-07 0 5.3916863e-06 5.4445277e-06 7.034379e-06 9.4285714 + 95900 5.8353112e-07 0 5.3864279e-06 5.4411008e-06 7.1207417e-06 9.4285714 + 96000 5.4965917e-07 0 5.3883171e-06 5.4521987e-06 7.207183e-06 9.4285714 + 96100 5.029591e-07 0 5.3992099e-06 5.4818384e-06 7.2609387e-06 9.4285714 + 96200 4.5561069e-07 0 5.4154371e-06 5.5240071e-06 7.2708316e-06 9.4285714 + 96300 4.3112225e-07 0 5.4307319e-06 5.5600285e-06 7.2500045e-06 9.4285714 + 96400 4.3930285e-07 0 5.4430151e-06 5.5789722e-06 7.2160611e-06 9.4285714 + 96500 4.6493378e-07 0 5.4661115e-06 5.5785143e-06 7.1781808e-06 9.4285714 + 96600 4.9251458e-07 0 5.4963377e-06 5.5640999e-06 7.1270969e-06 9.4285714 + 96700 5.0736557e-07 0 5.521707e-06 5.5498419e-06 7.0880266e-06 9.4285714 + 96800 5.0623403e-07 0 5.5421159e-06 5.5497869e-06 7.0876008e-06 9.4285714 + 96900 4.9644583e-07 0 5.5541079e-06 5.5554785e-06 7.0985488e-06 9.4285714 + 97000 4.9272012e-07 0 5.5642491e-06 5.5573245e-06 7.1072643e-06 9.4285714 + 97100 5.0766017e-07 0 5.574804e-06 5.5607502e-06 7.0960704e-06 9.4285714 + 97200 5.2395618e-07 0 5.5904541e-06 5.5972925e-06 7.0868355e-06 9.4285714 + 97300 4.9953435e-07 0 5.6118394e-06 5.6549726e-06 7.1004286e-06 9.4285714 + 97400 4.7056592e-07 0 5.6267739e-06 5.6665867e-06 7.132434e-06 9.4285714 + 97500 4.6366588e-07 0 5.6279978e-06 5.6384286e-06 7.1776822e-06 9.4285714 + 97600 4.6533884e-07 0 5.6201426e-06 5.6143272e-06 7.2143735e-06 9.4285714 + 97700 4.6375828e-07 0 5.6042233e-06 5.5922009e-06 7.2259013e-06 9.4285714 + 97800 4.5549968e-07 0 5.581613e-06 5.5683497e-06 7.2201315e-06 9.4285714 + 97900 4.4830148e-07 0 5.5561604e-06 5.5523988e-06 7.2080551e-06 9.4285714 + 98000 4.4229249e-07 0 5.5339104e-06 5.5493638e-06 7.1912426e-06 9.4285714 + 98100 4.3249616e-07 0 5.5169313e-06 5.5572061e-06 7.1620443e-06 9.4285714 + 98200 4.2277099e-07 0 5.5048256e-06 5.555431e-06 7.1279636e-06 9.4285714 + 98300 4.0884592e-07 0 5.4920455e-06 5.5364094e-06 7.088059e-06 9.4285714 + 98400 3.8363767e-07 0 5.4775359e-06 5.5080096e-06 7.05458e-06 9.4285714 + 98500 3.6073132e-07 0 5.4670069e-06 5.4816869e-06 7.0387787e-06 9.4285714 + 98600 3.4144123e-07 0 5.4706682e-06 5.4743026e-06 7.0537276e-06 9.4285714 + 98700 3.1616356e-07 0 5.4884314e-06 5.4787633e-06 7.0717401e-06 9.4285714 + 98800 2.9524387e-07 0 5.5116444e-06 5.4915117e-06 7.0801815e-06 9.4285714 + 98900 2.8085695e-07 0 5.5360366e-06 5.5192781e-06 7.0852811e-06 9.4285714 + 99000 2.7334761e-07 0 5.5583091e-06 5.5646801e-06 7.0905775e-06 9.4285714 + 99100 2.8302882e-07 0 5.5671736e-06 5.6102205e-06 7.0851405e-06 9.4285714 + 99200 3.0871833e-07 0 5.5626313e-06 5.641669e-06 7.0655021e-06 9.4285714 + 99300 3.2788327e-07 0 5.5501776e-06 5.6578835e-06 7.052597e-06 9.4285714 + 99400 3.270588e-07 0 5.5333145e-06 5.6580921e-06 7.0554426e-06 9.4285714 + 99500 3.0876961e-07 0 5.5137891e-06 5.6472952e-06 7.0790365e-06 9.4285714 + 99600 2.7792352e-07 0 5.492857e-06 5.630656e-06 7.1072011e-06 9.4285714 + 99700 2.4620411e-07 0 5.4730212e-06 5.6109129e-06 7.1194189e-06 9.4285714 + 99800 2.3278402e-07 0 5.464734e-06 5.5969326e-06 7.115628e-06 9.4285714 + 99900 2.394249e-07 0 5.4754248e-06 5.5974473e-06 7.1078477e-06 9.4285714 + 100000 2.4873051e-07 0 5.5011397e-06 5.6103192e-06 7.1032974e-06 9.4285714 +Loop time of 279.196 on 1 procs for 100000 steps with 2520 atoms + +Performance: 1547298.377 tau/day, 358.171 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 | 4.2815 | 4.2815 | 4.2815 | 0.0 | 1.53 +Bond | 250.07 | 250.07 | 250.07 | 0.0 | 89.57 +Neigh | 4.3874 | 4.3874 | 4.3874 | 0.0 | 1.57 +Comm | 0.1863 | 0.1863 | 0.1863 | 0.0 | 0.07 +Output | 0.091049 | 0.091049 | 0.091049 | 0.0 | 0.03 +Modify | 19.366 | 19.366 | 19.366 | 0.0 | 6.94 +Other | | 0.8108 | | | 0.29 + +Nlocal: 2520.00 ave 2520 max 2520 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 9814.00 ave 9814 max 9814 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9814 +Ave neighs/atom = 3.8944444 +Ave special neighs/atom = 36.317460 +Neighbor list builds = 4924 +Dangerous builds = 274 +Total wall time: 0:04:39 diff --git a/examples/bpm/pour/log.30Jul2021.pour.g++.1 b/examples/bpm/pour/log.30Jul2021.pour.g++.1 deleted file mode 100644 index eec316e8ae..0000000000 --- a/examples/bpm/pour/log.30Jul2021.pour.g++.1 +++ /dev/null @@ -1,1090 +0,0 @@ -LAMMPS (30 Jul 2021) -units lj -dimension 3 -boundary m m m -atom_style sphere/bpm -special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 -newton on off -comm_modify vel yes cutoff 3.3 -region box block -15 15 -15 15 0 60.0 -create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50 -Created orthogonal box = (-15.000000 -15.000000 0.0000000) to (15.000000 15.000000 60.000000) - 1 by 1 by 1 MPI processor grid - -molecule my_mol "rect.mol" -Read molecule template my_mol: - 1 molecules - 63 atoms with max type 1 - 297 bonds with max type 1 - 0 angles with max type 0 - 0 dihedrals with max type 0 - 0 impropers with max type 0 -region wall_cyl cylinder z 0.0 0.0 10.0 EDGE EDGE side in -region dropzone cylinder z 0.0 0.0 10.0 40.0 50.0 side in - -pair_style gran/hertz/history 1.0 NULL 0.5 NULL 0.1 1 -bond_style bpm/rotational -pair_coeff 1 1 -bond_coeff 1 1.0 0.2 0.01 0.01 2.0 0.4 0.02 0.02 0.2 0.04 0.002 0.002 - -compute nbond all nbond/atom -compute tbond all reduce sum c_nbond -compute_modify thermo_temp dynamic/dof yes - -fix 1 all wall/gran hertz/history 1.0 NULL 0.5 NULL 0.1 1 zplane 0.0 NULL -fix 2 all wall/gran/region hertz/history 1.0 NULL 0.5 NULL 0.1 1 region wall_cyl -fix 3 all gravity 1e-4 vector 0 0 -1 -fix 4 all deposit 40 0 1500 712511343 mol my_mol region dropzone near 2.0 vz -0.05 -0.05 -fix 5 all nve/sphere/bpm -fix 6 all update/special/bonds - -timestep 0.05 -thermo_style custom step ke pe pxx pyy pzz c_tbond -thermo 100 -dump 1 all custom 500 atomDump id radius x y z c_nbond mol - -run 100000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.3 - ghost atom cutoff = 3.3 - binsize = 0.65, bins = 47 47 93 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair gran/hertz/history, perpetual - attributes: half, newton on, size, history - pair build: half/size/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.510 | 7.510 | 7.510 Mbytes -Step KinEng PotEng Pxx Pyy Pzz c_tbond - 0 -0 0 0 0 0 0 - 100 0.0018350004 -4.7142847 -1.4952358e-05 -1.3419249e-05 -1.2232534e-06 9.4285714 - 200 0.0026448865 -4.7142836 2.4009175e-06 3.4985286e-06 4.4774541e-06 9.4285714 - 300 0.0037671165 -4.71428 7.7868315e-06 4.3344542e-06 5.2003707e-06 9.4285714 - 400 0.0060866155 -4.7142466 -2.6407137e-05 -4.6012096e-06 -7.2652236e-06 9.4285714 - 500 0.0074581085 -4.7142677 2.91441e-05 2.1596938e-05 1.7547302e-05 9.4285714 - 600 0.0078583344 -4.7142826 -1.5003346e-06 1.4512508e-05 2.9703819e-06 9.4285714 - 700 0.0075360513 -4.7142727 -2.5876771e-06 1.2941955e-05 1.8800678e-06 9.4285714 - 800 0.0073708697 -4.7142811 2.342014e-05 1.3677972e-05 1.7951529e-05 9.4285714 - 900 0.0075293135 -4.7142781 -1.0363878e-05 1.3616086e-05 -4.4997782e-06 9.4285714 - 1000 0.0075664914 -4.7142805 9.7952433e-06 1.4238252e-05 1.0500218e-05 9.4285714 - 1100 0.0075487959 -4.7142816 1.3144826e-05 1.4347122e-05 1.3503414e-05 9.4285714 - 1200 0.0075161044 -4.714269 -5.7314502e-06 9.4758079e-06 -3.9561706e-06 9.4285714 - 1300 0.0075736256 -4.7142839 1.1243108e-05 1.7774357e-05 1.3346305e-05 9.4285714 - 1400 0.0076065814 -4.7142688 6.0289115e-06 1.4598083e-05 8.0109348e-06 9.4285714 - 1500 0.0075850039 -4.7142836 9.8106843e-07 7.3175578e-06 1.3244496e-06 9.4285714 - 1600 0.0059673005 -4.7142772 5.4481504e-06 2.0461455e-05 1.0148563e-05 9.4285714 - 1700 0.008060977 -4.7142767 2.9012609e-06 2.2950155e-05 1.3486974e-06 9.4285714 - 1800 0.0087747918 -4.7142819 7.4904656e-06 3.6100052e-05 1.7017909e-05 9.4285714 - 1900 0.0087089259 -4.7142751 8.357802e-06 4.0019544e-05 1.680366e-05 9.4285714 - 2000 0.0087016626 -4.7142836 6.3761243e-06 2.3991468e-05 6.5215381e-06 9.4285714 - 2100 0.008427332 -4.7142785 9.6989453e-06 3.2889581e-05 1.6275771e-05 9.4285714 - 2200 0.0083664952 -4.7142818 7.176817e-06 3.0276432e-05 5.9757096e-06 9.4285714 - 2300 0.0083480746 -4.7142791 1.0583095e-05 2.448771e-05 1.3325786e-05 9.4285714 - 2400 0.0082989793 -4.7142829 1.2568526e-05 3.5256163e-05 1.3898753e-05 9.4285714 - 2500 0.0083834043 -4.714283 8.1815532e-06 2.6950039e-05 7.3853891e-06 9.4285714 - 2600 0.0084024866 -4.7142832 1.0774493e-05 2.8041987e-05 1.4089582e-05 9.4285714 - 2700 0.0083048258 -4.7142846 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-1.5615417e-05 9.4285714 - 98700 1.650016e-07 -4.7142857 -1.5071686e-05 -1.5871434e-05 -1.5646712e-05 9.4285714 - 98800 1.5381591e-07 -4.7142857 -1.4976039e-05 -1.5916557e-05 -1.5639779e-05 9.4285714 - 98900 1.4561701e-07 -4.7142857 -1.4948048e-05 -1.5942893e-05 -1.5591273e-05 9.4285714 - 99000 1.409876e-07 -4.7142857 -1.4938783e-05 -1.5964216e-05 -1.552527e-05 9.4285714 - 99100 1.3647033e-07 -4.7142857 -1.4929778e-05 -1.5954524e-05 -1.5435251e-05 9.4285714 - 99200 1.3362811e-07 -4.7142857 -1.493995e-05 -1.5899959e-05 -1.536751e-05 9.4285714 - 99300 1.332697e-07 -4.7142857 -1.4901845e-05 -1.5823408e-05 -1.5288535e-05 9.4285714 - 99400 1.3246942e-07 -4.7142857 -1.4863126e-05 -1.58044e-05 -1.5177726e-05 9.4285714 - 99500 1.2902143e-07 -4.7142857 -1.4839913e-05 -1.5850368e-05 -1.5096824e-05 9.4285714 - 99600 1.2026e-07 -4.7142857 -1.4783678e-05 -1.5936741e-05 -1.5045878e-05 9.4285714 - 99700 1.0682618e-07 -4.7142857 -1.4722651e-05 -1.6094168e-05 -1.5037704e-05 9.4285714 - 99800 1.0135835e-07 -4.7142857 -1.4653152e-05 -1.6166665e-05 -1.5083701e-05 9.4285714 - 99900 1.0408582e-07 -4.7142857 -1.4564358e-05 -1.6121388e-05 -1.5103438e-05 9.4285714 - 100000 1.0680034e-07 -4.7142857 -1.4507587e-05 -1.604874e-05 -1.5136253e-05 9.4285714 -Loop time of 290.919 on 1 procs for 100000 steps with 2520 atoms - -Performance: 1484950.148 tau/day, 343.738 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 5.4111 | 5.4111 | 5.4111 | 0.0 | 1.86 -Bond | 255.11 | 255.11 | 255.11 | 0.0 | 87.69 -Neigh | 4.7124 | 4.7124 | 4.7124 | 0.0 | 1.62 -Comm | 0.12616 | 0.12616 | 0.12616 | 0.0 | 0.04 -Output | 0.61128 | 0.61128 | 0.61128 | 0.0 | 0.21 -Modify | 24.262 | 24.262 | 24.262 | 0.0 | 8.34 -Other | | 0.6856 | | | 0.24 - -Nlocal: 2520.00 ave 2520 max 2520 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0.00000 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 9690.00 ave 9690 max 9690 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 9690 -Ave neighs/atom = 3.8452381 -Ave special neighs/atom = 36.317460 -Neighbor list builds = 5077 -Dangerous builds = 354 -Total wall time: 0:04:50 diff --git a/src/BPM/bond_bpm.cpp b/src/BPM/bond_bpm.cpp index 7ff883a140..04521cd0d8 100644 --- a/src/BPM/bond_bpm.cpp +++ b/src/BPM/bond_bpm.cpp @@ -34,7 +34,10 @@ using namespace LAMMPS_NS; BondBPM::BondBPM(LAMMPS *lmp) : Bond(lmp) { + id_fix_dummy = nullptr; + id_fix_dummy2 = nullptr; id_fix_store_local = nullptr; + id_fix_bond_history = nullptr; id_fix_prop_atom = nullptr; id_fix_update = nullptr; fix_store_local = nullptr; @@ -49,11 +52,15 @@ BondBPM::BondBPM(LAMMPS *lmp) : Bond(lmp) r0_max_estimate = 0.0; max_stretch = 1.0; - // create dummy fix as placeholder for FixUpdateSpecialBonds + // create dummy fix as placeholder for FixUpdateSpecialBonds & BondHistory // this is so final order of Modify:fix will conform to input script + // BondHistory technically only needs this if updateflag = 1 - id_fix_dummy = utils::strdup("BPM_DUMMY" + std::to_string(instance_me)); + id_fix_dummy = utils::strdup("BPM_DUMMY_" + std::to_string(instance_me)); modify->add_fix(fmt::format("{} all DUMMY ", id_fix_dummy)); + + id_fix_dummy2 = utils::strdup("BPM_DUMMY2_" + std::to_string(instance_me)); + modify->add_fix(fmt::format("{} all DUMMY ", id_fix_dummy2)); } /* ---------------------------------------------------------------------- */ @@ -63,12 +70,16 @@ BondBPM::~BondBPM() delete [] pack_choice; if (id_fix_dummy) modify->delete_fix(id_fix_dummy); + if (id_fix_dummy2) modify->delete_fix(id_fix_dummy2); if (id_fix_update) modify->delete_fix(id_fix_update); + if (id_fix_bond_history) modify->delete_fix(id_fix_bond_history); if (id_fix_store_local) modify->delete_fix(id_fix_store_local); if (id_fix_prop_atom) modify->delete_fix(id_fix_prop_atom); delete [] id_fix_dummy; + delete [] id_fix_dummy2; delete [] id_fix_update; + delete [] id_fix_bond_history; delete [] id_fix_store_local; delete [] id_fix_prop_atom; @@ -83,7 +94,7 @@ void BondBPM::init_style() if (id_fix_store_local) { ifix = modify->find_fix(id_fix_store_local); if (ifix < 0) error->all(FLERR, "Cannot find fix store/local"); - if (strcmp(modify->fix[ifix]->style, "store/local") != 0) + if (strcmp(modify->fix[ifix]->style, "STORE_LOCAL") != 0) error->all(FLERR, "Incorrect fix style matched, not store/local"); fix_store_local = (FixStoreLocal *) modify->fix[ifix]; fix_store_local->nvalues = nvalues; @@ -115,7 +126,7 @@ void BondBPM::init_style() error->all(FLERR,"Without overlay/pair, BPM bond sytles requires special Coulomb weights = 1,1,1"); if (id_fix_dummy) { - id_fix_update = utils::strdup("BPM_update_special_bonds" + std::to_string(instance_me)); + id_fix_update = utils::strdup("BPM_UPDATE_SPECIAL_BONDS_" + std::to_string(instance_me)); fix_update_special_bonds = (FixUpdateSpecialBonds *) modify->replace_fix(id_fix_dummy, fmt::format("{} all UPDATE_SPECIAL_BONDS", id_fix_update),1); delete [] id_fix_dummy; @@ -148,14 +159,14 @@ void BondBPM::settings(int narg, char **arg) { leftover_args.clear(); - int local_freq; int iarg = 0; while (iarg < narg) { if (strcmp(arg[iarg], "store/local") == 0) { nvalues = 0; - local_freq = utils::inumeric(FLERR, arg[iarg+1], false, lmp); + id_fix_store_local = utils::strdup(arg[iarg+1]); + store_local_freq = utils::inumeric(FLERR, arg[iarg+2], false, lmp); pack_choice = new FnPtrPack[narg - iarg - 1]; - iarg += 2; + iarg += 3; while (iarg < narg) { if (strcmp(arg[iarg], "id1") == 0) { pack_choice[nvalues++] = &BondBPM::pack_id1; @@ -181,7 +192,7 @@ void BondBPM::settings(int narg, char **arg) } else { break; } - iarg ++; + iarg ++; } } else if (strcmp(arg[iarg], "overlay/pair") == 0) { overlay_flag = 1; @@ -192,24 +203,31 @@ void BondBPM::settings(int narg, char **arg) } } - if (nvalues != 0 && !id_fix_store_local) { - //Todo, assign ID and create fix id_fix_store_local = utils::strdup(arg[iarg+1]); + if (id_fix_store_local) { if (nvalues == 0) error->all(FLERR, "Bond style bpm/rotational must include at least one value to output"); memory->create(output_data, nvalues, "bond/bpm:output_data"); - // Use store property to save reference positions as it can transfer to ghost atoms + int ifix = modify->find_fix(id_fix_store_local); + if (ifix < 0) { + modify->add_fix(fmt::format("{} all STORE_LOCAL {} {}", + id_fix_store_local, store_local_freq, nvalues)); + ifix = modify->find_fix(id_fix_store_local); + } + fix_store_local = (FixStoreLocal *) modify->fix[ifix]; + + // Use property/atom to save reference positions as it can transfer to ghost atoms // This won't work for instances where bonds are added (e.g. fix pour) but in those cases // a reference state isn't well defined if (prop_atom_flag == 1) { id_fix_prop_atom = utils::strdup("BPM_property_atom" + std::to_string(instance_me)); - int ifix = modify->find_fix(id_fix_prop_atom); - char *x_ref_id = utils::strdup("BPM_X_REF" + std::to_string(instance_me)); char *y_ref_id = utils::strdup("BPM_Y_REF" + std::to_string(instance_me)); char *z_ref_id = utils::strdup("BPM_Z_REF" + std::to_string(instance_me)); + + ifix = modify->find_fix(id_fix_prop_atom); if (ifix < 0) { modify->add_fix(fmt::format("{} all property/atom {} {} {} ghost yes", id_fix_prop_atom, x_ref_id, y_ref_id, z_ref_id)); diff --git a/src/BPM/bond_bpm.h b/src/BPM/bond_bpm.h index 3f71aefa45..24689e6f52 100644 --- a/src/BPM/bond_bpm.h +++ b/src/BPM/bond_bpm.h @@ -37,10 +37,12 @@ class BondBPM : public Bond { protected: double r0_max_estimate; double max_stretch; + int store_local_freq; std::vector leftover_args; - char *id_fix_dummy, *id_fix_update; + char *id_fix_dummy, *id_fix_dummy2; + char *id_fix_update, *id_fix_bond_history; char *id_fix_store_local, *id_fix_prop_atom; class FixStoreLocal *fix_store_local; class FixBondHistory *fix_bond_history; diff --git a/src/BPM/bond_bpm_rotational.cpp b/src/BPM/bond_bpm_rotational.cpp index 80fff550ee..ccc96d8fbc 100644 --- a/src/BPM/bond_bpm_rotational.cpp +++ b/src/BPM/bond_bpm_rotational.cpp @@ -44,8 +44,6 @@ BondBPMRotational::BondBPMRotational(LAMMPS *lmp) : BondBPM(lmp) BondBPMRotational::~BondBPMRotational() { - if (fix_bond_history) modify->delete_fix("BOND_HISTORY_BPM_ROTATIONAL"); - if (allocated) { memory->destroy(setflag); memory->destroy(Kr); @@ -641,9 +639,13 @@ void BondBPMRotational::init_style() if(domain->dimension == 2) error->warning(FLERR, "Bond style bpm/rotational not intended for 2d use"); - if (!fix_bond_history) - fix_bond_history = (FixBondHistory *) modify->add_fix( - "HISTORY_BPM_ROTATIONAL" + std::to_string(instance_me) + " all BOND_HISTORY 0 4"); + if (!id_fix_bond_history) { + id_fix_bond_history = utils::strdup("HISTORY_BPM_ROTATIONAL" + std::to_string(instance_me)); + fix_bond_history = (FixBondHistory *) modify->replace_fix(id_fix_dummy2, + fmt::format("{} all BOND_HISTORY 0 4", id_fix_bond_history),1); + delete [] id_fix_dummy2; + id_fix_dummy2 = nullptr; + } } /* ---------------------------------------------------------------------- */ diff --git a/src/BPM/bond_bpm_spring.cpp b/src/BPM/bond_bpm_spring.cpp index 021d552297..d43c18d1e7 100644 --- a/src/BPM/bond_bpm_spring.cpp +++ b/src/BPM/bond_bpm_spring.cpp @@ -39,8 +39,6 @@ BondBPMSpring::BondBPMSpring(LAMMPS *lmp) : BondBPM(lmp) BondBPMSpring::~BondBPMSpring() { - if (fix_bond_history) modify->delete_fix("BOND_HISTORY_BPM_SPRING"); - if (allocated) { memory->destroy(setflag); memory->destroy(k); @@ -277,9 +275,13 @@ void BondBPMSpring::init_style() if (comm->ghost_velocity == 0) error->all(FLERR,"Bond bpm/spring requires ghost atoms store velocity"); - if (!fix_bond_history) - fix_bond_history = (FixBondHistory *) modify->add_fix( - "HISTORY_BPM_SPRING_" + std::to_string(instance_me) + " all BOND_HISTORY 0 1"); + if (!id_fix_bond_history) { + id_fix_bond_history = utils::strdup("HISTORY_BPM_ROTATIONAL" + std::to_string(instance_me)); + fix_bond_history = (FixBondHistory *) modify->replace_fix(id_fix_dummy2, + fmt::format("{} all BOND_HISTORY 0 1", id_fix_bond_history),1); + delete [] id_fix_dummy2; + id_fix_dummy2 = nullptr; + } } /* ---------------------------------------------------------------------- */ diff --git a/src/MISC/pair_tracker.cpp b/src/MISC/pair_tracker.cpp index 3864ba6be7..4d372e959e 100644 --- a/src/MISC/pair_tracker.cpp +++ b/src/MISC/pair_tracker.cpp @@ -52,11 +52,12 @@ PairTracker::PairTracker(LAMMPS *lmp) : // create dummy fix as placeholder for FixNeighHistory // this is so final order of Modify:fix will conform to input script + id_fix_dummy = utils::strdup("TRACKER_DUMMY_" + std::to_string(instance_me)); + modify->add_fix(fmt::format("{} all DUMMY ", id_fix_dummy)); - fix_history = nullptr; - modify->add_fix("NEIGH_HISTORY_TRACK_DUMMY all DUMMY"); - fix_dummy = (FixDummy *) modify->fix[modify->nfix - 1]; - + id_fix_history = nullptr; + id_fix_store_local = nullptr; + fix_history = nullptr; fix_store_local = nullptr; output_data = nullptr; @@ -68,10 +69,9 @@ PairTracker::PairTracker(LAMMPS *lmp) : PairTracker::~PairTracker() { - if (!fix_history) - modify->delete_fix("NEIGH_HISTORY_TRACK_DUMMY"); - else - modify->delete_fix("NEIGH_HISTORY_TRACK"); + if (id_fix_dummy) modify->delete_fix(id_fix_dummy); + if (fix_history) modify->delete_fix(id_fix_history); + if (id_fix_store_local) modify->delete_fix(id_fix_store_local); if (allocated) { memory->destroy(setflag); @@ -86,7 +86,10 @@ PairTracker::~PairTracker() delete[] pack_choice; + delete[] id_fix_dummy; + delete[] id_fix_history; delete[] id_fix_store_local; + memory->destroy(output_data); memory->destroy(type_filter); } @@ -229,15 +232,16 @@ void PairTracker::allocate() void PairTracker::settings(int narg, char **arg) { - if (narg < 1) error->all(FLERR, "Illegal pair_style command"); + if (narg < 2) error->all(FLERR, "Illegal pair_style command"); id_fix_store_local = utils::strdup(arg[0]); + store_local_freq = utils::inumeric(FLERR, arg[1], false, lmp); // If optional arguments included, this will be oversized pack_choice = new FnPtrPack[narg - 1]; nvalues = 0; - int iarg = 1; + int iarg = 2; while (iarg < narg) { if (strcmp(arg[iarg], "finite") == 0) { finitecutflag = 1; @@ -306,6 +310,14 @@ void PairTracker::settings(int narg, char **arg) if (nvalues == 0) error->all(FLERR, "Must request at least one value to output"); memory->create(output_data, nvalues, "pair/tracker:output_data"); + + int ifix = modify->find_fix(id_fix_store_local); + if (ifix < 0) { + modify->add_fix(fmt::format("{} all STORE_LOCAL {} {}", + id_fix_store_local, store_local_freq, nvalues)); + ifix = modify->find_fix(id_fix_store_local); + } + fix_store_local = (FixStoreLocal *) modify->fix[ifix]; } /* ---------------------------------------------------------------------- @@ -343,7 +355,7 @@ void PairTracker::coeff(int narg, char **arg) void PairTracker::init_style() { - int i; + int i, ifix; // error and warning checks if (!atom->radius_flag && finitecutflag) @@ -363,17 +375,22 @@ void PairTracker::init_style() // it replaces FixDummy, created in the constructor // this is so its order in the fix list is preserved - if (fix_history == nullptr) { - modify->replace_fix("NEIGH_HISTORY_TRACK_DUMMY", - fmt::format("NEIGH_HISTORY_TRACK all NEIGH_HISTORY {}", size_history), 1); - int ifix = modify->find_fix("NEIGH_HISTORY_TRACK"); - fix_history = (FixNeighHistory *) modify->fix[ifix]; + if (id_fix_dummy) { + id_fix_history = utils::strdup("TRACKER_NEIGH_HIST_" + std::to_string(instance_me)); + fix_history = (FixNeighHistory *) modify->replace_fix(id_fix_dummy, + fmt::format("{} all NEIGH_HISTORY {}", id_fix_history, size_history), 1); fix_history->pair = this; fix_history->use_bit_flag = 0; + + delete [] id_fix_dummy; + id_fix_dummy = nullptr; + } else { + ifix = modify->find_fix(id_fix_history); + if (ifix < 0) error->all(FLERR, "Could not find pair fix neigh history ID"); + fix_history = (FixNeighHistory *) modify->fix[ifix]; } if (finitecutflag) { - if (force->pair->beyond_contact) error->all(FLERR, "Pair tracker incompatible with granular pairstyles that extend beyond contact"); @@ -425,18 +442,6 @@ void PairTracker::init_style() MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world); MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world); } - - int ifix = modify->find_fix("NEIGH_HISTORY_TRACK"); - if (ifix < 0) error->all(FLERR, "Could not find pair fix neigh history ID"); - fix_history = (FixNeighHistory *) modify->fix[ifix]; - - ifix = modify->find_fix(id_fix_store_local); - if (ifix < 0) error->all(FLERR, "Cannot find fix store/local"); - if (strcmp(modify->fix[ifix]->style, "store/local") != 0) - error->all(FLERR, "Incorrect fix style matched, not store/local"); - fix_store_local = (FixStoreLocal *) modify->fix[ifix]; - if (fix_store_local->nvalues != nvalues) - error->all(FLERR, "Inconsistent number of output variables in fix store/local"); } /* ---------------------------------------------------------------------- diff --git a/src/MISC/pair_tracker.h b/src/MISC/pair_tracker.h index 3be7e7ebc0..13a8709866 100644 --- a/src/MISC/pair_tracker.h +++ b/src/MISC/pair_tracker.h @@ -51,7 +51,10 @@ class PairTracker : public Pair { double *onerad_dynamic, *onerad_frozen; double *maxrad_dynamic, *maxrad_frozen; int freeze_group_bit; + int store_local_freq; + char *id_fix_dummy; + char *id_fix_history; char *id_fix_store_local; class FixDummy *fix_dummy; class FixNeighHistory *fix_history;