From d1442b0538d85e5890edbc52b512c356fb611143 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 4 Sep 2020 11:33:49 -0600 Subject: [PATCH] enable per-atom custom arrays in addition to vectors --- doc/src/balance.rst | 18 +- doc/src/compute_property_atom.rst | 117 ++++---- doc/src/dump.rst | 45 +-- doc/src/fix_property_atom.rst | 258 +++++++++-------- doc/src/fix_store_state.rst | 35 ++- doc/src/group.rst | 37 ++- doc/src/set.rst | 34 ++- src/Makefile | 1 + src/atom.cpp | 202 ++++++++++--- src/atom.h | 17 +- src/compute_property_atom.cpp | 171 +++++++---- src/compute_property_atom.h | 20 +- src/dump_custom.cpp | 279 +++++++++++------- src/dump_custom.h | 25 +- src/fix_group.cpp | 34 ++- src/fix_group.h | 2 +- src/fix_property_atom.cpp | 453 +++++++++++++++++++++--------- src/fix_property_atom.h | 9 +- src/fix_store_state.cpp | 199 ++++++++----- src/imbalance_store.cpp | 13 +- src/input.cpp | 53 +++- src/set.cpp | 88 ++++-- src/set.h | 2 +- 23 files changed, 1390 insertions(+), 722 deletions(-) diff --git a/doc/src/balance.rst b/doc/src/balance.rst index e023b6f2f0..afa43cbc2f 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -465,12 +465,18 @@ atom-style variables can reference the position of a particle, its velocity, the volume of its Voronoi cell, etc. The *store* weight style does not compute a weight factor. Instead it -stores the current accumulated weights in a custom per-atom property -specified by *name*\ . This must be a property defined as *d_name* via -the :doc:`fix property/atom ` command. Note that -these custom per-atom properties can be output in a :doc:`dump ` -file, so this is a way to examine, debug, or visualize the -per-particle weights computed during the load-balancing operation. +stores the current accumulated weights in a custom per-atom vector +specified by *name*\ . This must be a vector defined as *d_name* via +the :doc:`fix property/atom ` command. This means +the values in the vector can be read as part of a data file with the +:doc:`read_data ` command or specified with the :doc:`set +` command. These weights can also be output in a :doc:`dump +` file, so this is a way to examine, debug, or visualize the +per-particle weights used during the load-balancing operation. + +Note that the name of the custom per-atom vector is specified just +as *name*, not as *d_name* as it is for other commands that use +different kinds of custom atom vectors or arrays as arguments. ---------- diff --git a/doc/src/compute_property_atom.rst b/doc/src/compute_property_atom.rst index ec9322bb7b..b455b7ae53 100644 --- a/doc/src/compute_property_atom.rst +++ b/doc/src/compute_property_atom.rst @@ -20,7 +20,8 @@ Syntax x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, vx, vy, vz, fx, fy, fz, q, mux, muy, muz, mu, - sp, spx, spy, spz, fmx, fmy, fmz, + spx, spy, spz, sp, fmx, fmy, fmz, + nbonds, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, shapex,shapey, shapez, @@ -29,42 +30,42 @@ Syntax corner1x, corner1y, corner1z, corner2x, corner2y, corner2z, corner3x, corner3y, corner3z, - nbonds, - buckling, - vfrac, s0, - spin, eradius, ervel, erforce, - rho, drho, e, de, cv, - i_name, d_name + i_name, d_name, i2_name[I], d2_name[I], + vfrac, s0, spin, eradius, ervel, erforce, + rho, drho, e, de, cv, buckling .. parsed-literal:: - id = atom ID - mol = molecule ID - proc = ID of processor that owns atom - type = atom type - mass = atom mass - x,y,z = unscaled atom coordinates - xs,ys,zs = scaled atom coordinates - xu,yu,zu = unwrapped atom coordinates - ix,iy,iz = box image that the atom is in - vx,vy,vz = atom velocities - fx,fy,fz = forces on atoms - q = atom charge - mux,muy,muz = orientation of dipole moment of atom - mu = magnitude of dipole moment of atom - sp = atomic magnetic spin moment - spx, spy, spz = direction of the atomic magnetic spin - fmx, fmy, fmz = magnetic force - radius,diameter = radius,diameter of spherical particle - omegax,omegay,omegaz = angular velocity of spherical particle - angmomx,angmomy,angmomz = angular momentum of aspherical particle - shapex,shapey,shapez = 3 diameters of aspherical particle - quatw,quati,quatj,quatk = quaternion components for aspherical or body particles - tqx,tqy,tqz = torque on finite-size particles - end12x, end12y, end12z = end points of line segment - corner123x, corner123y, corner123z = corner points of triangle - nbonds = number of bonds assigned to an atom - buckling = buckling flag used in mesoscopic simulation of nanotubes + *id* = atom ID + *mol* = molecule ID + *proc* = ID of processor that owns atom + *type* = atom type + *mass* = atom mass + *x,y,z* = unscaled atom coordinates + *xs,ys,zs* = scaled atom coordinates + *xu,yu,zu* = unwrapped atom coordinates + *ix,iy,iz* = box image that the atom is in + *vx,vy,vz* = atom velocities + *fx,fy,fz* = forces on atoms + *q* = atom charge + *mux,muy,muz* = orientation of dipole moment of atom + *mu* = magnitude of dipole moment of atom + *spx, spy, spz* = direction of the atomic magnetic spin + *sp* = magintude of atomic magnetic spin moment + *fmx, fmy, fmz* = magnetic force + *nbonds* = number of bonds assigned to an atom + *radius,diameter* = radius,diameter of spherical particle + *omegax,omegay,omegaz* = angular velocity of spherical particle + *angmomx,angmomy,angmomz* = angular momentum of aspherical particle + *shapex,shapey,shapez* = 3 diameters of aspherical particle + *quatw,quati,quatj,quatk* = quaternion components for aspherical or body particles + *tqx,tqy,tqz* = torque on finite-size particles + *end12x, end12y, end12z* = end points of line segment + *corner123x, corner123y, corner123z* = corner points of triangle + *i_name* = custom integer vector with name + *d_name* = custom floating point vector with name + *i2_name[I]* = Ith column of custom integer array with name + *d2_name[I]* = Ith column of custom floating-point array with name .. parsed-literal:: @@ -91,9 +92,8 @@ Syntax .. parsed-literal:: - :doc:`fix property/atom ` per-atom properties: - i_name = custom integer vector with name - d_name = custom integer vector with name + USER-MESONT package per-atom properties: + buckling = buckling flag used in mesoscopic simulation of nanotubes Examples """""""" @@ -104,6 +104,7 @@ Examples compute 2 all property/atom type compute 1 all property/atom ix iy iz compute 3 all property/atom sp spx spy spz + compute 1 all property/atom i_myFlag d_Sxyz[1] d_Sxyz[3] Description """"""""""" @@ -116,20 +117,37 @@ ave/atom `, :doc:`fix ave/histo `, :doc:`fix ave/chunk `, and :doc:`atom-style variable ` commands. -The list of possible attributes is the same as that used by the -:doc:`dump custom ` command, which describes their meaning, with -some additional quantities that are only defined for certain -:doc:`atom styles `. Basically, this augmented list gives -an input script access to any per-atom quantity stored by LAMMPS. +The list of possible attributes is essentially the same as that used +by the :doc:`dump custom ` command, which describes their +meaning, with some additional quantities that are only defined for +certain :doc:`atom styles `. The goal of this augmented +list gives an input script access to any per-atom quantity stored by +LAMMPS. The values are stored in a per-atom vector or array as discussed below. Zeroes are stored for atoms not in the specified group or for quantities that are not defined for a particular particle in the group (e.g. *shapex* if the particle is not an ellipsoid). +Attributes *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom +per-atom integer and floating-point vectors or arrays that have been +added via the :doc:`fix property/atom ` command. +When that command is used specific names are given to each attribute +which are the "name" portion of these attributes. For arrays *i2_name* +and *d2_name*, the column of the array must also be included following +the name in brackets: e.g. d2_xyz[2], i2_mySpin[3]. + The additional quantities only accessible via this command, and not directly via the :doc:`dump custom ` command, are as follows. +*Nbonds* is available for all molecular atom styles and refers to the +number of explicit bonds assigned to an atom. Note that if the +:doc:`newton bond ` command is set to *on*\ , which is the +default, then every bond in the system is assigned to only one of the +two atoms in the bond. Thus a bond between atoms I,J may be tallied +for either atom I or atom J. If :doc:`newton bond off ` is +set, it will be tallied with both atom I and atom J. + *Shapex*\ , *shapey*\ , and *shapez* are defined for ellipsoidal particles and define the 3d shape of each particle. @@ -146,19 +164,8 @@ line segment. *corner2z*\ , *corner3x*\ , *corner3y*\ , *corner3z*\ , are defined for triangular particles and define the corner points of each triangle. -*Nbonds* is available for all molecular atom styles and refers to the -number of explicit bonds assigned to an atom. Note that if the -:doc:`newton bond ` command is set to *on*\ , which is the -default, then every bond in the system is assigned to only one of the -two atoms in the bond. Thus a bond between atoms I,J may be tallied -for either atom I or atom J. If :doc:`newton bond off ` is -set, it will be tallied with both atom I and atom J. - -The *i_name* and *d_name* attributes refer to custom integer and -floating-point properties that have been added to each atom via the -:doc:`fix property/atom ` command. When that -command is used specific names are given to each attribute which are -what is specified as the "name" portion of *i_name* or *d_name*. +In addition, the various per-atom quantities listed above for specific +packages are only accessible by this command. Output info """"""""""" diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 36a20defb6..2b7e6d7bae 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -78,7 +78,8 @@ Syntax q, mux, muy, muz, mu, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, tqx, tqy, tqz, - c_ID, c_ID[N], f_ID, f_ID[N], v_name + c_ID, c_ID[I], f_ID, f_ID[I], v_name, + i_name, d_name, i2_name[I], d2_name[I] .. parsed-literal:: @@ -108,8 +109,10 @@ Syntax f_ID = per-atom vector calculated by a fix with ID f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) v_name = per-atom vector calculated by an atom-style variable with name - d_name = per-atom floating point vector with name, managed by fix property/atom - i_name = per-atom integer vector with name, managed by fix property/atom + i_name = custom integer vector with name + d_name = custom floating point vector with name + i2_name[I] = Ith column of custom integer array with name, I can include wildcard (see below) + d2_name[I] = Ith column of custom floating point vector with name, I can include wildcard (see below) * *local* args = list of local attributes @@ -134,7 +137,7 @@ Examples dump 2 subgroup atom 50 dump.run.mpiio.bin dump 4a all custom 100 dump.myforce.* id type x y vx fx dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke - dump 4b flow custom 100 dump.%.myforce id type c_myF[\*] v_ke + dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2] dump 1 all xtc 1000 file.xtc @@ -465,16 +468,15 @@ styles. ---------- Note that in the discussion which follows, for styles which can -reference values from a compute or fix, like the *custom*\ , *cfg*\ , or -*local* styles, the bracketed index I can be specified using a -wildcard asterisk with the index to effectively specify multiple -values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the -size of the vector (for *mode* = scalar) or the number of columns in -the array (for *mode* = vector), then an asterisk with no numeric -values means all indices from 1 to N. A leading asterisk means all -indices from 1 to n (inclusive). A trailing asterisk means all -indices from n to N (inclusive). A middle asterisk means all indices -from m to n (inclusive). +reference values from a compute or fix or custom atom property, like +the *custom*\ , *cfg*\ , or *local* styles, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form "\*" or "\*n" or "n\*" +or "m\*n". If N = the number of columns in the array, then an +asterisk with no numeric values means all column indices from 1 to N. +A leading asterisk means all indices from 1 to n (inclusive). A +trailing asterisk means all indices from n to N (inclusive). A middle +asterisk means all indices from m to n (inclusive). Using a wildcard is the same as if the individual columns of the array had been listed one by one. E.g. these 2 dump commands are @@ -512,8 +514,9 @@ bonds and angles. Note that computes which calculate global or per-atom quantities, as opposed to local quantities, cannot be output in a dump local command. -Instead, global quantities can be output by the :doc:`thermo_style custom ` command, and per-atom quantities can be -output by the dump custom command. +Instead, global quantities can be output by the :doc:`thermo_style +custom ` command, and per-atom quantities can be output +by the dump custom command. If *c_ID* is used as a attribute, then the local vector calculated by the compute is printed. If *c_ID[I]* is used, then I must be in the @@ -660,9 +663,13 @@ invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of creating quantities to output to a dump file. -The *d_name* and *i_name* attributes allow to output custom per atom -floating point or integer properties that are managed by -:doc:`fix property/atom `. +The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to +per-atom integer and floating-point vectors or arrays that have been +added via the :doc:`fix property/atom ` command. +When that command is used specific names are given to each attribute +which are the "name" portion of these keywords. For arrays *i2_name* +and *d2_name*, the column of the array must also be included following +the name in brackets: e.g. d2_xyz[2], i2_mySpin[3]. See the :doc:`Modify ` doc page for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index eaf246c1a3..584451cba1 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -11,11 +11,11 @@ Syntax .. parsed-literal:: - fix ID group-ID property/atom vec1 vec2 ... keyword value ... + fix ID group-ID property/atom name1 name2 ... keyword value ... * ID, group-ID are documented in :doc:`fix ` command * property/atom = style name of this fix command -* vec1,vec2,... = *mol* or *q* or *rmass* or *i_name* or *d_name* +* name1,name2,... = *mol* or *q* or *rmass* or *i_name* or *d_name* or *i2_name* or *d2_name* .. parsed-literal:: @@ -24,6 +24,10 @@ Syntax *rmass* = per-atom mass *i_name* = new integer vector referenced by name *d_name* = new floating-point vector referenced by name + *i2_name* = new integer array referenced by name + i2_name arg = N = number of columns in the array + *d2_name* = new floating-point array referenced by name + d2_name arg = N = number of columns in the array * zero of more keyword/value pairs may be appended * keyword = *ghost* @@ -39,58 +43,64 @@ Examples fix 1 all property/atom mol fix 1 all property/atom i_myflag1 i_myflag2 - fix 1 all property/atom d_sx d_sy d_sz + fix 1 all property/atom d2_sxyz 3 ghost yes Description """"""""""" -Create one or more additional per-atom vectors to store information -about atoms and to use during a simulation. The specified *group-ID* -is ignored by this fix. +Create one or more additional per-atom vectors or arrays to store +information about atoms and to use during a simulation. The specified +*group-ID* is ignored by this fix. The atom style used for a simulation defines a set of per-atom properties, as explained on the :doc:`atom_style ` and -:doc:`read_data ` doc pages. The latter command allows these -properties to be defined for each atom in the system when a data file -is read. This fix will augment the set of properties with new custom +:doc:`read_data ` doc pages. The latter command defines +these properties for each atom in the system when a data file is read. +This fix augments the set of per-atom properties with new custom ones. This can be useful in several scenarios. -If the atom style does not define molecule IDs, per-atom charge, -or per-atom mass, they can be added using the *mol*\ , *q* or *rmass* -keywords. This can be useful, e.g, to define "molecules" to use as -rigid bodies with the :doc:`fix rigid ` command, or just to -carry around an extra flag with the atoms (stored as a molecule ID) -that can be used to group atoms without having to use the group +If the atom style does not define molecule IDs, per-atom charge, or +per-atom mass, they can be added using the *mol*\ , *q* or *rmass* +keywords. This ciykd be useful to define "molecules" to use as rigid +bodies with the :doc:`fix rigid ` command, or to carry +around an extra flag with atoms (stored as a molecule ID) that can be +used by various commands like :doc:`compute chunk/atom +` to group atoms without having to use the group command (which is limited to a total of 32 groups including *all*\ ). -Another application would be to use the *rmass* flag in order to have -per-atom masses instead of per-type masses, for example this can be -useful to study isotope effects with partial isotope substitution. -Please :ref:`see below ` for an example of simulating a mixture -of light and heavy water with the TIP4P water potential. +Another application is to use the *rmass* flag in order to have +per-atom masses instead of per-type masses. This could be used to +study isotope effects with partial isotope substitution. :ref:`See +below ` for an example of simulating a mixture of light and +heavy water with the TIP4P water potential. -An alternative to using fix *property/atom* in these ways is to +An alternative to using fix *property/atom* for these examples is to use an atom style that does define molecule IDs or charge or per-atom mass (indirectly via diameter and density) or to use a hybrid atom -style that combines two or more atom styles -to provide the union of all atom properties. However, this has two -practical drawbacks: first, it typically necessitates changing the -format of the data file, which can be tedious for large systems; -and second, it may define additional properties that are not needed -such as bond lists, which has some overhead when there are no bonds. +style that combines two or more atom styles to provide the union of +all their atom properties. However, this has two practical drawbacks: +first, it typically necessitates changing the format of the Atoms +section in the data file and second, it may define additional +properties that are not needed such as bond lists, which incurs some +overhead when there are no bonds. -In the future, we may add additional per-atom properties similar to -*mol*\ , *q* or *rmass*\ , which "turn-on" specific properties defined -by some atom styles, so they can be used by atom styles that do not -define them. +In the future, we may add additional existing per-atom properties to +fix property/atom, similar to *mol*\ , *q* or *rmass*\ , which +"turn-on" specific properties defined by some atom styles, so they can +be easily used by atom styles that do not define them. -More generally, the *i_name* and *d_name* vectors allow one or more -new custom per-atom properties to be defined. Each name must be -unique and can use alphanumeric or underscore characters. These -vectors can store whatever values you decide are useful in your -simulation. As explained below there are several ways to initialize -and access and output these values, both via input script commands and -in new code that you add to LAMMPS. +More generally, the *i_name* and *d_name* options allow one or more +new custom per-atom vectors to be defined. Likewise the *i2_name* and +*d2_name* options allow one or more custom per-atom arrays to be +defined. The *i2_name* and *d2_name* options take an argument *N* +which specifies the number of columns in the per-atom array, i.e. the +number of attributes associated with each atom. *N* >= 1 is required. + +Each name must be unique and can use alphanumeric or underscore +characters. These vectors and arrays can store whatever values you +decide are useful in your simulation. As explained below there are +several ways to initialize, access, and output these values, via input +script commands, data files, and in new code you add to LAMMPS. This is effectively a simple way to add per-atom properties to a model without needing to write code for a new :doc:`atom style ` @@ -107,42 +117,38 @@ new properties are also defined for the ghost atoms. .. note:: - If you use this command with the *mol*\ , *q* or *rmass* vectors, - then you most likely want to set *ghost* yes, since these properties - are stored with ghost atoms if you use an :doc:`atom_style ` - that defines them, and many LAMMPS operations that use molecule IDs or - charge, such as neighbor lists and pair styles, will expect ghost - atoms to have these values. LAMMPS will issue a warning it you define - those vectors but do not set *ghost* yes. + If you use the *mol*\ , *q* or *rmass* names, you most likely want + to set *ghost* yes, since these properties are stored with ghost + atoms if you use an :doc:`atom_style ` that defines + them. Many LAMMPS operations that use molecule IDs or charge, such + as neighbor lists and pair styles, will expect ghost atoms to have + these values. LAMMPS will issue a warning it you define those + vectors but do not set *ghost* yes. .. note:: - The properties for ghost atoms are not updated every timestep, - but only once every few steps when neighbor lists are re-built. Thus - the *ghost* keyword is suitable for static properties, like molecule - IDs, but not for dynamic properties that change every step. For the - latter, the code you add to LAMMPS to change the properties will also - need to communicate their new values to/from ghost atoms, an operation - that can be invoked from within a :doc:`pair style ` or - :doc:`fix ` or :doc:`compute ` that you write. - -.. note:: - - If this fix is defined **after** the simulation box is created, - a 'run 0' command should be issued to properly initialize the storage - created by this fix. + The specified properties for ghost atoms are not updated every + timestep, but only once every few steps when neighbor lists are + re-built. Thus the *ghost* keyword is suitable for static + properties, like molecule IDs, but not for dynamic properties that + change every step. For the latter, the code you add to LAMMPS to + change the properties will also need to communicate their new + values to/from ghost atoms, an operation that can be invoked from + within a :doc:`pair style ` or :doc:`fix ` or + :doc:`compute ` that you write. ---------- This fix is one of a small number that can be defined in an input script before the simulation box is created or atoms are defined. -This is so it can be used with the :doc:`read_data ` command -as described below. +This is so it can be used with the :doc:`read_data ` +command as described next. -Per-atom properties that are defined by the :doc:`atom style ` are initialized when atoms are created, e.g. by -the :doc:`read_data ` or :doc:`create_atoms ` +Per-atom properties that are defined by the :doc:`atom style +` are initialized when atoms are created, e.g. by the +:doc:`read_data ` or :doc:`create_atoms ` commands. The per-atom properties defined by this fix are not. So -you need to initialize them explicitly. This can be done by the +you need to initialize them explicitly. One way to do thisis :doc:`read_data ` command, using its *fix* keyword and passing it the fix-ID of this fix. @@ -167,15 +173,22 @@ would allow a data file to have a section like this: ... N 763 4.5 -where N is the number of atoms, and the first field on each line is -the atom-ID, followed by a molecule-ID and a floating point value that -will be stored in a new property called "flag". Note that the list of -per-atom properties can be in any order. +where N is the number of atoms, the first field on each line is the +atom-ID, the next two are a molecule-ID and a floating point value +that will be stored in a new property called "flag". If a per-atom +array was specified in the fix property/atom commmand then the *N* +values for that array must be specified consecutively for that +property on each line. -Another way of initializing the new properties is via the -:doc:`set ` command. For example, if you wanted molecules -defined for every set of 10 atoms, based on their atom-IDs, -these commands could be used: +Note that the the lines of per-atom properties can be listed in any +order. Also note that all the per-atom properties specified by the +fix ID (prop in this case) must be included on each line in the +specified data file section (Molecules in this case). + +Another way of initializing the new properties is via the :doc:`set +` command. For example, if you wanted molecules defined for +every set of 10 atoms, based on their atom-IDs, these commands could +be used: .. code-block:: LAMMPS @@ -185,53 +198,59 @@ these commands could be used: The :doc:`atom-style variable ` will create values for atoms with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9. When the -:doc:`set ` commands assigns them to the molecule ID for each atom, -they will be truncated to an integer value, so atoms 31-40 will all be -assigned a molecule ID of 4. +:doc:`set ` commands assigns them to the molecule ID for each +atom, they will be truncated to an integer value, so atoms 31-40 will +all be assigned a molecule ID of 4. -Note that :doc:`atomfile-style variables ` can also be used in -place of atom-style variables, which means in this case that the +Note that :doc:`atomfile-style variables ` can also be used +in place of atom-style variables, which means in this case that the molecule IDs could be read-in from a separate file and assigned by the :doc:`set ` command. This allows you to initialize new per-atom properties in a completely general fashion. ---------- -For new atom properties specified as *i_name* or *d_name*, the -:doc:`compute property/atom ` command can access -their values. This means that the values can be output via the :doc:`dump custom ` command, accessed by fixes like :doc:`fix ave/atom `, accessed by other computes like :doc:`compute reduce `, or used in :doc:`atom-style variables `. +For new atom properties specified as *i_name*, *d_name*, *i2_name*, or +*d2_name*, the :doc:`dump custom ` and :doc:`compute +property/atom ` commands can access their +values. This means that the values can be used accessed by fixes like +:doc:`fix ave/atom `, accessed by other computes like +:doc:`compute reduce `, or used in :doc:`atom-style +variables `. -For example, these commands will output two new properties to a custom -dump file: +For example, these commands will output both the instantanous and +time-averaged values of two new properties to a custom dump file: .. code-block:: LAMMPS - fix prop all property/atom i_flag1 d_flag2 + fix myprops all property/atom i_flag1 d_flag2 compute 1 all property/atom i_flag1 d_flag2 - dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2] + fix 1 all ave/atom 10 10 100 c_1[1] c_1[2] + dump 1 all custom 100 tmp.dump id x y z i_flag1 d_flag2 f_1[1] f_1[2] ---------- -If you wish to add new :doc:`pair styles `, -:doc:`fixes `, or :doc:`computes ` that use the per-atom -properties defined by this fix, see the :doc:`Modify atom ` -doc page which has details on how the properties can be accessed from -added classes. +If you wish to add new :doc:`pair styles `, :doc:`fixes +`, or :doc:`computes ` that use the per-atom properties +defined by this fix, see the :doc:`Modify atom ` doc page +which has details on how the custom properties of this fix can be +accessed from added classes. ---------- .. _isotopes: -Example for using per-atom masses with TIP4P water to -study isotope effects. When setting up simulations with the :doc:`TIP4P pair styles ` for water, you have to provide exactly -one atom type each to identify the water oxygen and hydrogen -atoms. Since the atom mass is normally tied to the atom type, this -makes it impossible to study multiple isotopes in the same simulation. -With *fix property/atom rmass* however, the per-type masses are -replaced by per-atom masses. Asumming you have a working input deck -for regular TIP4P water, where water oxygen is atom type 1 and water -hydrogen is atom type 2, the following lines of input script convert -this to using per-atom masses: +Here is an example of using per-atom masses with TIP4P water to study +isotope effects. When setting up simulations with the :doc:`TIP4P pair +styles ` for water, you have to provide exactly one atom +type each to identify the water oxygen and hydrogen atoms. Since the +atom mass is normally tied to the atom type, this makes it impossible +to study multiple isotopes in the same simulation. With *fix +property/atom rmass* however, the per-type masses are replaced by +per-atom masses. Asumming you have a working input deck for regular +TIP4P water, where water oxygen is atom type 1 and water hydrogen is +atom type 2, the following lines of input script convert this to using +per-atom masses: .. code-block:: LAMMPS @@ -239,22 +258,22 @@ this to using per-atom masses: set type 1 mass 15.9994 set type 2 mass 1.008 -When writing out the system data with the :doc:`write_data ` -command, there will be a new section named with the fix-ID -(i.e. *Isotopes* in this case). Alternatively, you can take an -existing data file and just add this *Isotopes* section with -one line per atom containing atom-ID and mass. Either way, the -extended data file can be read back with: +When writing out the system data with the :doc:`write_data +` command, there will be a new section named with the +fix-ID (i.e. *Isotopes* in this case). Alternatively, you can take an +existing data file and just add this *Isotopes* section with one line +per atom containing atom-ID and mass. Either way, the extended data +file can be read back with: .. code-block:: LAMMPS fix Isotopes all property/atom rmass ghost yes read_data tip4p-isotopes.data fix Isotopes NULL Isotopes -Please note that the first *Isotopes* refers to the fix-ID -and the second to the name of the section. The following input -script code will now change the first 100 water molecules in this -example to heavy water: +Please note that the first *Isotopes* refers to the fix-ID and the +second to the name of the section. The following input script code +will now change the first 100 water molecules in this example to heavy +water: .. code-block:: LAMMPS @@ -271,17 +290,19 @@ example to heavy water: Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -This fix writes the per-atom values it stores to :doc:`binary restart files `, so that the values can be restored when a -simulation is restarted. See the :doc:`read_restart ` -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an +This fix writes the per-atom values it stores to :doc:`binary restart +files `, so that the values can be restored when a simulation +is restarted. See the :doc:`read_restart ` command for +info on how to re-specify a fix in an input script that reads a +restart file, so that the operation of the fix continues in an uninterrupted fashion. -None of the :doc:`fix_modify ` options are relevant to this -fix. No global or per-atom quantities are stored by this fix for +None of the :doc:`fix_modify ` options are relevant to +this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the -:doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. +:doc:`run ` command. This fix is not invoked during :doc:`energy +minimization `. Restrictions """""""""""" @@ -290,9 +311,10 @@ Restrictions Related commands """""""""""""""" -:doc:`read_data `, :doc:`set `, :doc:`compute property/atom ` +:doc:`read_data `, :doc:`set `, +:doc:`compute property/atom ` Default """"""" -The default keyword values are ghost = no. +The default keyword value is ghost = no. diff --git a/doc/src/fix_store_state.rst b/doc/src/fix_store_state.rst index 5f42e3ef5d..dee46e2086 100644 --- a/doc/src/fix_store_state.rst +++ b/doc/src/fix_store_state.rst @@ -23,8 +23,8 @@ Syntax q, mux, muy, muz, mu, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, tqx, tqy, tqz, - c_ID, c_ID[N], f_ID, f_ID[N], v_name, - d_name, i_name + c_ID, c_ID[I], f_ID, f_ID[I], v_name, + d_name, i_name, i2_name[I], d2_name[I], .. parsed-literal:: @@ -46,13 +46,15 @@ Syntax omegax,omegay,omegaz = angular velocity of spherical particle angmomx,angmomy,angmomz = angular momentum of aspherical particle tqx,tqy,tqz = torque on finite-size particles - c_ID = per-atom vector calculated by a compute with ID - c_ID[I] = Ith column of per-atom array calculated by a compute with ID - f_ID = per-atom vector calculated by a fix with ID - f_ID[I] = Ith column of per-atom array calculated by a fix with ID - v_name = per-atom vector calculated by an atom-style variable with name - d_name = per-atom floating point vector name, managed by fix property/atom - i_name = per-atom integer vector name, managed by fix property/atom + *c_ID* = per-atom vector calculated by a compute with ID + *c_ID[I]* = Ith column of per-atom array calculated by a compute with ID + *f_ID* = per-atom vector calculated by a fix with ID + *f_ID[I]* = Ith column of per-atom array calculated by a fix with ID + *v_name* = per-atom vector calculated by an atom-style variable with name + *i_name* = custom integer vector with name + *d_name* = custom floating point vector with name + *i2_name[I]* = Ith column of custom integer array with name + *d2_name[I]* = Ith column of custom floating-point array with name * zero or more keyword/value pairs may be appended * keyword = *com* @@ -92,7 +94,8 @@ steps. those attributes may require quantities that are not defined in between runs. -The list of possible attributes is the same as that used by the :doc:`dump custom ` command, which describes their meaning. +The list of possible attributes is the same as that used by the +:doc:`dump custom ` command, which describes their meaning. If the *com* keyword is set to *yes* then the *xu*\ , *yu*\ , and *zu* inputs store the position of each atom relative to the center-of-mass @@ -105,10 +108,11 @@ group. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -This fix writes the per-atom values it stores to :doc:`binary restart files `, so that the values can be restored when a -simulation is restarted. See the :doc:`read_restart ` -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an +This fix writes the per-atom values it stores to :doc:`binary restart +files `, so that the values can be restored when a simulation +is restarted. See the :doc:`read_restart ` command for +info on how to re-specify a fix in an input script that reads a +restart file, so that the operation of the fix continues in an uninterrupted fashion. None of the :doc:`fix_modify ` options are relevant to this @@ -121,7 +125,8 @@ can be accessed by various :doc:`output commands `. The per-atom values be accessed on any timestep. No parameter of this fix can be used with the *start/stop* keywords of -the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. +the :doc:`run ` command. This fix is not invoked during +:doc:`energy minimization `. Restrictions """""""""""" diff --git a/doc/src/group.rst b/doc/src/group.rst index 6371a030ee..61690c4d42 100644 --- a/doc/src/group.rst +++ b/doc/src/group.rst @@ -41,7 +41,7 @@ Syntax keyword = *region* or *var* or *every* *region* value = region-ID *var* value = name of variable - *property* value = name of per-atom property + *property* value = name of custom integer or floating point vector *every* value = N = update group every this many timesteps *static* = no args @@ -226,18 +226,33 @@ simulation runs. This is in contrast to static groups where atoms are permanently assigned to the group. The way the assignment occurs is as follows. Only atoms in the group specified as the parent group via the parent-ID are assigned to the dynamic group before the following -conditions are applied. If the *region* keyword is used, atoms not in -the specified region are removed from the dynamic group. If the *var* -keyword is used, the variable name must be an atom-style or -atomfile-style variable. The variable is evaluated and atoms whose -per-atom values are 0.0, are removed from the dynamic group. If the *property* -keyword is used, the per-atom property name must be a previously defined -per-atom property. The per-atom property is evaluated and atoms whose -values are 0.0 are removed from the dynamic group. +conditions are applied. + +If the *region* keyword is used, atoms not in the specified region are +removed from the dynamic group. + +If the *var* keyword is used, the variable name must be an atom-style +or atomfile-style variable. The variable is evaluated and atoms whose +per-atom values are 0.0, are removed from the dynamic group. + +If the *property* keyword is used, the name refers to a custom integer +or floating point per-atom vector defined via the :doc:`fix +property/atom ` command. This means the values in +the vector can be read as part of a data file with the :doc:`read_data +` command or specified with the :doc:`set ` command. +Or accessed and changed via the :doc:`library interface to LAMMPS +`, or by styles you add to LAMMPS (pair, fix, compute, +etc) which access the custom vector and modify its values. Which +means the values can be modified between or during simulations. Atoms +whose values in the custom vector are zero are removed from the +dynamic group. Note that the name of the custom per-atom vector is +specified just as *name*, not as *i_name* or *d_name* as it is for +other commands that use different kinds of custom atom vectors or +arrays as arguments. The assignment of atoms to a dynamic group is done at the beginning of -each run and on every timestep that is a multiple of *N*\ , which is the -argument for the *every* keyword (N = 1 is the default). For an +each run and on every timestep that is a multiple of *N*\ , which is +the argument for the *every* keyword (N = 1 is the default). For an energy minimization, via the :doc:`minimize ` command, an assignment is made at the beginning of the minimization, but not during the iterations of the minimizer. diff --git a/doc/src/set.rst b/doc/src/set.rst index f830149569..82b577ca9f 100644 --- a/doc/src/set.rst +++ b/doc/src/set.rst @@ -13,7 +13,17 @@ Syntax * style = *atom* or *type* or *mol* or *group* or *region* * ID = atom ID range or type range or mol ID range or group ID or region ID * one or more keyword/value pairs may be appended -* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset* or *mol* or *x* or *y* or *z* or *charge* or *dipole* or *dipole/random* or *quat* or *spin* or *spin/random* or *quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or *theta* or *theta/random* or *angmom* or *omega* or *mass* or *density* or *density/disc* or *volume* or *image* or *bond* or *angle* or *dihedral* or *improper* or *sph/e* or *sph/cv* or *sph/rho* or *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or *edpd/temp* or *edpd/cv* or *cc* or *i_name* or *d_name* +* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset* + or *mol* or *x* or *y* or *z* or *charge* or *dipole* or + *dipole/random* or *quat* or *spin* or *spin/random* or + *quat* or *quat/random* or *diameter* or *shape* or + *length* or *tri* or *theta* or *theta/random* or *angmom* or + *omega* or *mass* or *density* or *density/disc* or + *volume* or *image* or *bond* or *angle* or *dihedral* or + *improper* or *sph/e* or *sph/cv* or *sph/rho* or + *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or + *edpd/temp* or *edpd/cv* or *cc* or + *i_name* or *d_name* or *i2_name* or *d2_name* .. parsed-literal:: @@ -114,8 +124,12 @@ Syntax *cc* values = index cc index = index of a chemical species (1 to Nspecies) cc = chemical concentration of tDPD particles for a species (mole/volume units) - *i_name* value = value for custom integer vector with name - *d_name* value = value for custom floating-point vector with name + *i_name* value = custom integer vector with name + *d_name* value = custom floating-point vector with name + *i2_name* value = column of a custom integer array with name + column specified as i2_name[N] where N is 1 to Ncol + *d2_name* value = column of a custom floating-point array with name + column specified as d2_name[N] where N is 1 to Ncol Examples """""""" @@ -132,6 +146,8 @@ Examples set atom 100*200 x 0.5 y 1.0 set atom 100 vx 0.0 vy 0.0 vz -1.0 set atom 1492 type 3 + set atom * i_myVal 5 + set atom * d2_Sxyz[1] 6.4 Description """"""""""" @@ -473,11 +489,13 @@ attribute. An integer for "index" selects a chemical species (1 to Nspecies) where Nspecies is set by the atom_style command. The value for the chemical concentration must be >= 0.0. -Keywords *i_name* and *d_name* refer to custom integer and -floating-point properties that have been added to each atom via the -:doc:`fix property/atom ` command. When that command -is used specific names are given to each attribute which are what is -specified as the "name" portion of *i_name* or *d_name*. +Keywords *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom +per-atom integer and floating-point vectors or arrays that have been +added via the :doc:`fix property/atom ` command. +When that command is used specific names are given to each attribute +which are the "name" portion of these keywords. For arrays *i2_name* +and *d2_name*, the column of the array must also be included following +the name in brackets: e.g. d2_xyz[2], i2_mySpin[3]. Restrictions """""""""""" diff --git a/src/Makefile b/src/Makefile index 4528c027cf..80d0a91a98 100644 --- a/src/Makefile +++ b/src/Makefile @@ -260,6 +260,7 @@ clean: clean-all: rm -rf Obj_* + rm style_*.h packages_*.h lmpgitversion.h lmpinstalledpkgs.h clean-%: @if [ $@ = "clean-serial" ]; \ diff --git a/src/atom.cpp b/src/atom.cpp index e930a0255e..4e2b82fb30 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -178,10 +178,13 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) // custom atom arrays - nivector = ndvector = 0; + nivector = ndvector = niarray = ndarray = 0; ivector = NULL; dvector = NULL; - iname = dname = NULL; + iarray = NULL; + darray = NULL; + icols = dcols = NULL; + ivname = dvname = ianame = daname = NULL; // initialize atom style and array existence flags @@ -262,20 +265,32 @@ Atom::~Atom() // delete custom atom arrays for (int i = 0; i < nivector; i++) { - delete [] iname[i]; + delete [] ivname[i]; memory->destroy(ivector[i]); } - if (dvector != NULL) { - for (int i = 0; i < ndvector; i++) { - delete [] dname[i]; - memory->destroy(dvector[i]); - } + for (int i = 0; i < ndvector; i++) { + delete [] dvname[i]; + memory->destroy(dvector[i]); + } + for (int i = 0; i < niarray; i++) { + delete [] ianame[i]; + memory->destroy(iarray[i]); + } + for (int i = 0; i < ndarray; i++) { + delete [] daname[i]; + memory->destroy(darray[i]); } - memory->sfree(iname); - memory->sfree(dname); + memory->sfree(ivname); + memory->sfree(dvname); + memory->sfree(ianame); + memory->sfree(daname); memory->sfree(ivector); memory->sfree(dvector); + memory->sfree(iarray); + memory->sfree(darray); + memory->sfree(icols); + memory->sfree(dcols); // delete user-defined molecules @@ -2282,23 +2297,41 @@ void Atom::update_callback(int ifix) /* ---------------------------------------------------------------------- find custom per-atom vector with name - return index if found, and flag = 0/1 for int/double - return -1 if not found + return index if found, -1 if not found + lists of names can have NULL entries if previously removed + return flag = 0/1 for int/double + return cols = 0/N for vector/array where N = # of columns ------------------------------------------------------------------------- */ -int Atom::find_custom(const char *name, int &flag) +int Atom::find_custom(const char *name, int &flag, int &cols) { - if(name == NULL) return -1; + if (name == NULL) return -1; for (int i = 0; i < nivector; i++) - if (iname[i] && strcmp(iname[i],name) == 0) { + if (ivname[i] && strcmp(ivname[i],name) == 0) { flag = 0; + cols = 0; return i; } for (int i = 0; i < ndvector; i++) - if (dname[i] && strcmp(dname[i],name) == 0) { + if (dvname[i] && strcmp(dvname[i],name) == 0) { flag = 1; + cols = 0; + return i; + } + + for (int i = 0; i < niarray; i++) + if (ianame[i] && strcmp(ianame[i],name) == 0) { + flag = 0; + cols = icols[i]; + return i; + } + + for (int i = 0; i < ndarray; i++) + if (daname[i] && strcmp(daname[i],name) == 0) { + flag = 1; + cols = dcols[i]; return i; } @@ -2306,60 +2339,107 @@ int Atom::find_custom(const char *name, int &flag) } /* ---------------------------------------------------------------------- - add a custom variable with name of type flag = 0/1 for int/double + add a custom variable with name + flag = 0/1 for int/double, cols = 0/N for vector/array where N = # of columns assumes name does not already exist - return index in ivector or dvector of its location + vectors of names and data ptrs are always incremented by one + return index in vector/array lists of its location ------------------------------------------------------------------------- */ -int Atom::add_custom(const char *name, int flag) +int Atom::add_custom(const char *name, int flag, int cols) { int index; - if (flag == 0) { + if (flag == 0 && cols == 0) { index = nivector; nivector++; - iname = (char **) memory->srealloc(iname,nivector*sizeof(char *), - "atom:iname"); + ivname = (char **) memory->srealloc(ivname,nivector*sizeof(char *), + "atom:ivname"); int n = strlen(name) + 1; - iname[index] = new char[n]; - strcpy(iname[index],name); + ivname[index] = new char[n]; + strcpy(ivname[index],name); ivector = (int **) memory->srealloc(ivector,nivector*sizeof(int *), "atom:ivector"); memory->create(ivector[index],nmax,"atom:ivector"); - } else { + + } else if (flag == 1 && cols == 0) { index = ndvector; ndvector++; - dname = (char **) memory->srealloc(dname,ndvector*sizeof(char *), - "atom:dname"); + dvname = (char **) memory->srealloc(dvname,ndvector*sizeof(char *), + "atom:dvname"); int n = strlen(name) + 1; - dname[index] = new char[n]; - strcpy(dname[index],name); + dvname[index] = new char[n]; + strcpy(dvname[index],name); dvector = (double **) memory->srealloc(dvector,ndvector*sizeof(double *), "atom:dvector"); memory->create(dvector[index],nmax,"atom:dvector"); - } + } else if (flag == 0 && cols) { + index = niarray; + niarray++; + ianame = (char **) memory->srealloc(ianame,niarray*sizeof(char *), + "atom:ianame"); + int n = strlen(name) + 1; + ianame[index] = new char[n]; + strcpy(ianame[index],name); + iarray = (int ***) memory->srealloc(iarray,niarray*sizeof(int **), + "atom:iarray"); + memory->create(iarray[index],nmax,cols,"atom:iarray"); + + icols = (int *) memory->srealloc(icols,niarray*sizeof(int),"atom:icols"); + icols[index] = cols; + + } else if (flag == 1 && cols) { + index = ndarray; + ndarray++; + daname = (char **) memory->srealloc(daname,ndarray*sizeof(char *), + "atom:daname"); + int n = strlen(name) + 1; + daname[index] = new char[n]; + strcpy(daname[index],name); + darray = (double ***) memory->srealloc(darray,ndarray*sizeof(double **), + "atom:darray"); + memory->create(darray[index],nmax,cols,"atom:darray"); + + dcols = (int *) memory->srealloc(dcols,ndarray*sizeof(int),"atom:dcols"); + dcols[index] = cols; + } + return index; } /* ---------------------------------------------------------------------- - remove a custom variable of type flag = 0/1 for int/double at index - free memory for vector and name and set ptrs to NULL - ivector/dvector and iname/dname lists never shrink + remove a custom variable stored at index + flag = 0/1 for int/double, cols = 0/1 for vector/array or N for array columns + free memory for vector/array and name and set ptrs to NULL + vector/array lists and name lists never shrink ------------------------------------------------------------------------- */ -void Atom::remove_custom(int flag, int index) +void Atom::remove_custom(int index, int flag, int cols) { - if (flag == 0) { + if (flag == 0 && cols == 0) { memory->destroy(ivector[index]); ivector[index] = NULL; - delete [] iname[index]; - iname[index] = NULL; - } else { + delete [] ivname[index]; + ivname[index] = NULL; + + } else if (flag == 1 && cols == 0) { memory->destroy(dvector[index]); dvector[index] = NULL; - delete [] dname[index]; - dname[index] = NULL; + delete [] dvname[index]; + dvname[index] = NULL; + + } else if (flag == 0 && cols) { + memory->destroy(iarray[index]); + iarray[index] = NULL; + delete [] ianame[index]; + ianame[index] = NULL; + + } else if (flag == 1 && cols) { + memory->destroy(darray[index]); + darray[index] = NULL; + delete [] daname[index]; + daname[index] = NULL; } } @@ -2372,7 +2452,8 @@ void *Atom::extract(char *name) { // -------------------------------------------------------------------- // 4th customization section: customize by adding new variable name - + // if new variable is from a package, add package comment + if (strcmp(name,"mass") == 0) return (void *) mass; if (strcmp(name,"id") == 0) return (void *) tag; @@ -2415,10 +2496,30 @@ void *Atom::extract(char *name) if (strcmp(name,"cv") == 0) return (void *) cv; if (strcmp(name,"vest") == 0) return (void *) vest; - // USER-MESONT package - if (strcmp(name,"length") == 0) return (void *) length; - if (strcmp(name,"buckling") == 0) return (void *) buckling; - if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt; + // custom vectors and arrays + + if (strstr(name,"i_") == name || strstr(name,"d_") == name || + strstr(name,"i2_") == name || strstr(name,"d2_") == name) { + int which = 0; + if (name[0] == 'd') which = 1; + int array = 0; + if (name[1] == '2') array = 1; + + int index,flag,cols; + if (!array) index = find_custom(&name[2],flag,cols); + else index = find_custom(&name[3],flag,cols); + + if (index < 0) return NULL; + if (which != flag) return NULL; + if ((!array && cols) || (array && !cols)) return NULL; + + if (!which && !array) return (void *) ivector[index]; + if (which && !array) return (void *) dvector[index]; + if (!which && array) return (void *) iarray[index]; + if (which && array) return (void *) darray[index]; + } + + // USER-SMD package if (strcmp(name, "contact_radius") == 0) return (void *) contact_radius; if (strcmp(name, "smd_data_9") == 0) return (void *) smd_data_9; @@ -2429,9 +2530,20 @@ void *Atom::extract(char *name) return (void *) eff_plastic_strain_rate; if (strcmp(name, "damage") == 0) return (void *) damage; + // USER-DPD package + if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta; + + // USER-MESO package + if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp; + // USER-MESONT package + + if (strcmp(name,"length") == 0) return (void *) length; + if (strcmp(name,"buckling") == 0) return (void *) buckling; + if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt; + // end of customization section // -------------------------------------------------------------------- diff --git a/src/atom.h b/src/atom.h index 4dac15d758..a2e69e06f2 100644 --- a/src/atom.h +++ b/src/atom.h @@ -206,12 +206,13 @@ class Atom : protected Pointers { PerAtom *peratom; int nperatom,maxperatom; - // custom arrays used by fix property/atom + // custom vectors and arrays used by fix property/atom - int **ivector; - double **dvector; - char **iname,**dname; - int nivector,ndvector; + int **ivector,***iarray; + double **dvector,***darray; + int *icols,*dcols; + char **ivname,**dvname,**ianame,**daname; + int nivector,ndvector,niarray,ndarray; // molecule templates // each template can be a set of consecutive molecules @@ -321,9 +322,9 @@ class Atom : protected Pointers { void delete_callback(const char *, int); void update_callback(int); - int find_custom(const char *, int &); - virtual int add_custom(const char *, int); - virtual void remove_custom(int, int); + int find_custom(const char *, int &, int &); + virtual int add_custom(const char *, int, int); + virtual void remove_custom(int, int, int); virtual void sync_modify(ExecutionSpace, unsigned int, unsigned int) {} diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp index 9c637edc1e..173665154c 100644 --- a/src/compute_property_atom.cpp +++ b/src/compute_property_atom.cpp @@ -24,6 +24,7 @@ #include "update.h" #include "domain.h" #include "comm.h" +#include "utils.h" #include "memory.h" #include "error.h" @@ -33,7 +34,7 @@ using namespace LAMMPS_NS; ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), - index(NULL), pack_choice(NULL) + index(NULL), colindex(NULL), pack_choice(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute property/atom command"); @@ -47,6 +48,7 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) : pack_choice = new FnPtrPack[nvalues]; index = new int[nvalues]; + colindex = new int[nvalues]; int i; for (int iarg = 3; iarg < narg; iarg++) { @@ -141,7 +143,10 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute property/atom for " "atom property that isn't allocated"); pack_choice[i] = &ComputePropertyAtom::pack_mu; - } else if (strcmp(arg[iarg],"spx") == 0) { // pack magnetic variables + + // pack magnetic variables + + } else if (strcmp(arg[iarg],"spx") == 0) { if (!atom->sp_flag) error->all(FLERR,"Compute property/atom for " "atom property that isn't allocated"); @@ -176,6 +181,17 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute property/atom for " "atom property that isn't allocated"); pack_choice[i] = &ComputePropertyAtom::pack_fmz; + + // bond count + + } else if (strcmp(arg[iarg],"nbonds") == 0) { + if (!atom->molecule_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_nbonds; + + // finite-size particles + } else if (strcmp(arg[iarg],"radius") == 0) { if (!atom->radius_flag) error->all(FLERR,"Compute property/atom for " @@ -329,6 +345,7 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) : if (!avec_tri) error->all(FLERR,"Compute property/atom for " "atom property that isn't allocated"); pack_choice[i] = &ComputePropertyAtom::pack_corner2x; + } else if (strcmp(arg[iarg],"corner2y") == 0) { avec_tri = (AtomVecTri *) atom->style_match("tri"); if (!avec_tri) error->all(FLERR,"Compute property/atom for " @@ -355,40 +372,59 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) : "atom property that isn't allocated"); pack_choice[i] = &ComputePropertyAtom::pack_corner3z; - } else if (strcmp(arg[iarg],"nbonds") == 0) { - if (!atom->molecule_flag) - error->all(FLERR,"Compute property/atom for " - "atom property that isn't allocated"); - pack_choice[i] = &ComputePropertyAtom::pack_nbonds; - + // custom per-atom vectors + } else if (strstr(arg[iarg],"i_") == arg[iarg]) { - int flag; - index[i] = atom->find_custom(&arg[iarg][2],flag); - if (index[i] < 0 || flag != 0) - error->all(FLERR,"Compute property/atom integer " - "vector does not exist"); + int flag,cols; + index[i] = atom->find_custom(&arg[iarg][2],flag,cols); + if (index[i] < 0 || flag || cols) + error->all(FLERR,"Compute property/atom custom vector does not exist"); pack_choice[i] = &ComputePropertyAtom::pack_iname; } else if (strstr(arg[iarg],"d_") == arg[iarg]) { - int flag; - index[i] = atom->find_custom(&arg[iarg][2],flag); - if (index[i] < 0 || flag != 1) - error->all(FLERR,"Compute property/atom floating point " - "vector does not exist"); + int flag,cols; + index[i] = atom->find_custom(&arg[iarg][2],flag,cols); + if (index[i] < 0 || !flag || cols) + error->all(FLERR,"Compute property/atom custom vector does not exist"); pack_choice[i] = &ComputePropertyAtom::pack_dname; - } - else if (strcmp(arg[iarg],"buckling") == 0) { - if (!atom->mesont_flag) - error->all(FLERR,"Compute property/atom for " - "atom property that isn't allocated"); - pack_choice[i] = &ComputePropertyAtom::pack_buckling; - // check if atom style recognizes keyword + // custom per-atom arrays, must include bracketed index + + } else if (strstr(arg[iarg],"i2_") == arg[iarg] || + strstr(arg[iarg],"d2_") == arg[iarg]) { + int which = 0; + if (arg[iarg][0] == 'd') which = 1; + + int n = strlen(arg[iarg]); + char *suffix = new char[n]; + strcpy(suffix,&arg[iarg][3]); + + char *ptr = strchr(suffix,'['); + if (ptr) { + if (suffix[strlen(suffix)-1] != ']') + error->all(FLERR,"Invalid attribute in set command"); + suffix[strlen(suffix)-1] = '\0'; + colindex[i] = utils::inumeric(FLERR,ptr+1,true,lmp); + *ptr = '\0'; + } else error->all(FLERR,"Compute property/atom custom array is not indexed"); + + int flag,cols; + index[i] = atom->find_custom(suffix,flag,cols); + delete [] suffix; + + if ((!which && (index[i] < 0 || flag || !cols)) || + (which && (index[i] < 0 || !flag || !cols))) + error->all(FLERR,"Compute property/atom custom array does not exist"); + + if (!which) pack_choice[i] = &ComputePropertyAtom::pack_i2name; + else pack_choice[i] = &ComputePropertyAtom::pack_d2name; + + // anything else must be recognized by atom style } else { index[i] = atom->avec->property_atom(arg[iarg]); if (index[i] < 0) error->all(FLERR,"Invalid keyword in compute property/atom command"); - pack_choice[i] = &ComputePropertyAtom::pack_property_atom; + pack_choice[i] = &ComputePropertyAtom::pack_atom_style; } } @@ -401,6 +437,7 @@ ComputePropertyAtom::~ComputePropertyAtom() { delete [] pack_choice; delete [] index; + delete [] colindex; memory->destroy(vector_atom); memory->destroy(array_atom); } @@ -413,6 +450,9 @@ void ComputePropertyAtom::init() avec_line = (AtomVecLine *) atom->style_match("line"); avec_tri = (AtomVecTri *) atom->style_match("tri"); avec_body = (AtomVecBody *) atom->style_match("body"); + + // NOTE: could reset custom vector/array indices here, like dump custom does + // in case have been deleted } /* ---------------------------------------------------------------------- */ @@ -1145,6 +1185,21 @@ void ComputePropertyAtom::pack_fmz(int n) /* ---------------------------------------------------------------------- */ +void ComputePropertyAtom::pack_nbonds(int n) +{ + int *num_bond = atom->num_bond; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = num_bond[i]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + void ComputePropertyAtom::pack_radius(int n) { double *radius = atom->radius; @@ -1780,36 +1835,6 @@ void ComputePropertyAtom::pack_corner3z(int n) /* ---------------------------------------------------------------------- */ -void ComputePropertyAtom::pack_buckling(int n) -{ - int *buckling = atom->buckling; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = static_cast(buckling[i]); - else buf[n] = 0.0; - n += nvalues; - } -} - -/* ---------------------------------------------------------------------- */ - -void ComputePropertyAtom::pack_nbonds(int n) -{ - int *num_bond = atom->num_bond; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = num_bond[i]; - else buf[n] = 0.0; - n += nvalues; - } -} - -/* ---------------------------------------------------------------------- */ - void ComputePropertyAtom::pack_iname(int n) { int *ivector = atom->ivector[index[n]]; @@ -1840,7 +1865,39 @@ void ComputePropertyAtom::pack_dname(int n) /* ---------------------------------------------------------------------- */ -void ComputePropertyAtom::pack_property_atom(int n) +void ComputePropertyAtom::pack_i2name(int n) +{ + int **iarray = atom->iarray[index[n]]; + int icol = colindex[n] - 1; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = iarray[i][icol]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyAtom::pack_d2name(int n) +{ + double **darray = atom->darray[index[n]]; + int icol = colindex[n] - 1; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = darray[i][icol]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyAtom::pack_atom_style(int n) { atom->avec->pack_property_atom(index[n],&buf[n],nvalues,groupbit); } diff --git a/src/compute_property_atom.h b/src/compute_property_atom.h index cab9d3ea1b..2b087204d2 100644 --- a/src/compute_property_atom.h +++ b/src/compute_property_atom.h @@ -35,7 +35,7 @@ class ComputePropertyAtom : public Compute { private: int nvalues; int nmax; - int *index; + int *index,*colindex; double *buf; class AtomVecEllipsoid *avec_ellipsoid; class AtomVecLine *avec_line; @@ -81,10 +81,6 @@ class ComputePropertyAtom : public Compute { void pack_muy(int); void pack_muz(int); void pack_mu(int); - void pack_radius(int); - void pack_diameter(int); - - // pack magnetic variables void pack_spx(int); void pack_spy(int); @@ -94,12 +90,17 @@ class ComputePropertyAtom : public Compute { void pack_fmy(int); void pack_fmz(int); + void pack_nbonds(int); + + void pack_radius(int); + void pack_diameter(int); void pack_omegax(int); void pack_omegay(int); void pack_omegaz(int); void pack_angmomx(int); void pack_angmomy(int); void pack_angmomz(int); + void pack_shapex(int); void pack_shapey(int); void pack_shapez(int); @@ -110,12 +111,14 @@ class ComputePropertyAtom : public Compute { void pack_tqx(int); void pack_tqy(int); void pack_tqz(int); + void pack_end1x(int); void pack_end1y(int); void pack_end1z(int); void pack_end2x(int); void pack_end2y(int); void pack_end2z(int); + void pack_corner1x(int); void pack_corner1y(int); void pack_corner1z(int); @@ -125,14 +128,13 @@ class ComputePropertyAtom : public Compute { void pack_corner3x(int); void pack_corner3y(int); void pack_corner3z(int); - void pack_buckling(int); - - void pack_nbonds(int); void pack_iname(int); void pack_dname(int); + void pack_i2name(int); + void pack_d2name(int); - void pack_property_atom(int); + void pack_atom_style(int); }; } diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 3297ecb4e7..2f89991c93 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -30,6 +30,7 @@ #include "update.h" #include "variable.h" #include "fmt/format.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -44,7 +45,7 @@ enum{ID,MOL,PROC,PROCP1,TYPE,ELEMENT,MASS, Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER, OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ, TQX,TQY,TQZ, - COMPUTE,FIX,VARIABLE,INAME,DNAME}; + COMPUTE,FIX,VARIABLE,IVEC,DVEC,IARRAY,DARRAY}; enum{LT,LE,GT,GE,EQ,NEQ,XOR}; #define INVOKED_PERATOM 8 @@ -60,7 +61,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) : earg(NULL), vtype(NULL), vformat(NULL), columns(NULL), choose(NULL), dchoose(NULL), clist(NULL), field2index(NULL), argindex(NULL), id_compute(NULL), compute(NULL), id_fix(NULL), fix(NULL), id_variable(NULL), variable(NULL), - vbuf(NULL), id_custom(NULL), flag_custom(NULL), typenames(NULL), + vbuf(NULL), id_custom(NULL), custom(NULL), custom_flag(NULL), typenames(NULL), pack_choice(NULL) { if (narg == 5) error->all(FLERR,"No dump custom arguments specified"); @@ -119,7 +120,8 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) : ncustom = 0; id_custom = NULL; - flag_custom = NULL; + custom = NULL; + custom_flag = NULL; // process attributes // ioptional = start of additional optional args in expanded args @@ -236,7 +238,8 @@ DumpCustom::~DumpCustom() for (int i = 0; i < ncustom; i++) delete [] id_custom[i]; memory->sfree(id_custom); - delete [] flag_custom; + delete [] custom; + delete [] custom_flag; memory->destroy(choose); memory->destroy(dchoose); @@ -324,7 +327,7 @@ void DumpCustom::init_style() else if (buffer_flag == 1) write_choice = &DumpCustom::write_string; else write_choice = &DumpCustom::write_lines; - // find current ptr for each compute,fix,variable + // find current ptr for each compute,fix,variable and custom atom property // check that fix frequency is acceptable int icompute; @@ -353,9 +356,15 @@ void DumpCustom::init_style() int icustom; for (int i = 0; i < ncustom; i++) { - icustom = atom->find_custom(id_custom[i],flag_custom[i]); + int flag,cols; + icustom = atom->find_custom(id_custom[i],flag,cols); if (icustom < 0) - error->all(FLERR,"Could not find custom per-atom property ID"); + error->all(FLERR,"Could not find dump custom atom property name"); + custom[i] = icustom; + if (!flag && !cols) custom_flag[i] = IVEC; + else if (flag && !cols) custom_flag[i] = DVEC; + else if (!flag && cols) custom_flag[i] = IARRAY; + else if (flag && cols) custom_flag[i] = DARRAY; } // set index and check validity of region @@ -1036,23 +1045,37 @@ int DumpCustom::count() ptr = vbuf[field2index[i]]; nstride = 1; - } else if (thresh_array[ithresh] == DNAME) { - int iwhich,tmp; + } else if (thresh_array[ithresh] == IVEC) { i = nfield + ithresh; - iwhich = atom->find_custom(id_custom[field2index[i]],tmp); - ptr = atom->dvector[iwhich]; - nstride = 1; - - } else if (thresh_array[ithresh] == INAME) { - int iwhich,tmp; - i = nfield + ithresh; - iwhich = atom->find_custom(id_custom[field2index[i]],tmp); - + int iwhich = custom[field2index[i]]; int *ivector = atom->ivector[iwhich]; for (i = 0; i < nlocal; i++) dchoose[i] = ivector[i]; ptr = dchoose; nstride = 1; + + } else if (thresh_array[ithresh] == DVEC) { + i = nfield + ithresh; + int iwhich = custom[field2index[i]]; + ptr = atom->dvector[iwhich]; + nstride = 1; + + } else if (thresh_array[ithresh] == IARRAY) { + i = nfield + ithresh; + int iwhich = custom[field2index[i]]; + int **iarray = atom->iarray[iwhich]; + int icol = argindex[i] - 1; + for (i = 0; i < nlocal; i++) + dchoose[i] = iarray[i][icol]; + ptr = dchoose; + nstride = 1; + + } else if (thresh_array[ithresh] == DARRAY) { + i = nfield + ithresh; + int iwhich = custom[field2index[i]]; + double **darray = atom->darray[iwhich]; + ptr = &darray[0][argindex[i]-1]; + nstride = atom->dcols[iwhich]; } // unselect atoms that don't meet threshold criterion @@ -1257,7 +1280,7 @@ int DumpCustom::parse_fields(int narg, char **arg) int i; for (int iarg = 0; iarg < narg; iarg++) { i = iarg; - + if (strcmp(arg[iarg],"id") == 0) { pack_choice[i] = &DumpCustom::pack_id; if (sizeof(tagint) == sizeof(smallint)) vtype[i] = Dump::INT; @@ -1455,7 +1478,8 @@ int DumpCustom::parse_fields(int narg, char **arg) if (ptr) { if (suffix[strlen(suffix)-1] != ']') error->all(FLERR,"Invalid attribute in dump custom command"); - argindex[i] = atoi(ptr+1); + suffix[strlen(suffix)-1] = '\0'; + argindex[i] = utils::inumeric(FLERR,ptr+1,true,lmp); *ptr = '\0'; } else argindex[i] = 0; @@ -1491,7 +1515,8 @@ int DumpCustom::parse_fields(int narg, char **arg) if (ptr) { if (suffix[strlen(suffix)-1] != ']') error->all(FLERR,"Invalid attribute in dump custom command"); - argindex[i] = atoi(ptr+1); + suffix[strlen(suffix)-1] = '\0'; + argindex[i] = utils::inumeric(FLERR,ptr+1,true,lmp); *ptr = '\0'; } else argindex[i] = 0; @@ -1530,48 +1555,66 @@ int DumpCustom::parse_fields(int narg, char **arg) field2index[i] = add_variable(suffix); delete [] suffix; - // custom per-atom floating point value = d_ID + // custom per-atom vector = i_ID or d_ID - } else if (strncmp(arg[iarg],"d_",2) == 0) { + } else if (strncmp(arg[iarg],"i_",2) == 0 || + strncmp(arg[iarg],"d_",2) == 0) { + int which = 0; + if (arg[iarg][0] == 'd') which = 1; + pack_choice[i] = &DumpCustom::pack_custom; - vtype[i] = Dump::DOUBLE; + if (!which) vtype[i] = Dump::INT; + else vtype[i] = Dump::DOUBLE; int n = strlen(arg[iarg]); char *suffix = new char[n]; strcpy(suffix,&arg[iarg][2]); argindex[i] = 0; - int tmp = -1; - n = atom->find_custom(suffix,tmp); - if (n < 0) - error->all(FLERR,"Could not find custom per-atom property ID"); + int flag,cols; + n = atom->find_custom(suffix,flag,cols); + if ((!which && (n < 0 || flag || cols)) || + (which && (n < 0 || !flag || cols))) + error->all(FLERR,"Dump custom per-atom custom vector does not exist"); - if (tmp != 1) - error->all(FLERR,"Custom per-atom property ID is not floating point"); - - field2index[i] = add_custom(suffix,1); + field2index[i] = add_custom(suffix); delete [] suffix; - // custom per-atom integer value = i_ID + // custom per-atom array = i2_ID or d2_ID, must include bracketed index + + } else if (strncmp(arg[iarg],"i2_",3) == 0 || + strncmp(arg[iarg],"d2_",3) == 0) { + int which = 0; + if (arg[iarg][0] == 'd') which = 1; - } else if (strncmp(arg[iarg],"i_",2) == 0) { pack_choice[i] = &DumpCustom::pack_custom; - vtype[i] = Dump::INT; + if (!which) vtype[i] = Dump::INT; + else vtype[i] = Dump::DOUBLE; int n = strlen(arg[iarg]); char *suffix = new char[n]; - strcpy(suffix,&arg[iarg][2]); - argindex[i] = 0; + strcpy(suffix,&arg[iarg][3]); - int tmp = -1; - n = atom->find_custom(suffix,tmp); - if (n < 0) - error->all(FLERR,"Could not find custom per-atom property ID"); + char *ptr = strchr(suffix,'['); + if (ptr) { + if (suffix[strlen(suffix)-1] != ']') + error->all(FLERR,"Invalid attribute in dump custom command"); + suffix[strlen(suffix)-1] = '\0'; + argindex[i] = utils::inumeric(FLERR,ptr+1,true,lmp); + *ptr = '\0'; + } else error->all(FLERR,"Dump custom per-atom custom array is not indexed"); - if (tmp != 0) - error->all(FLERR,"Custom per-atom property ID is not integer"); + int flag,cols; + n = atom->find_custom(suffix,flag,cols); + + if ((!which && (n < 0 || flag || !cols)) || + (which && (n < 0 || !flag || !cols))) + error->all(FLERR,"Dump custom per-atom custom array does not exist"); + if (argindex[i] <= 0 || argindex[i] > cols) + error->all(FLERR, + "Dump custom per-atom custom array is accessed out-of-range"); - field2index[i] = add_custom(suffix,0); + field2index[i] = add_custom(suffix); delete [] suffix; } else return iarg; @@ -1645,7 +1688,7 @@ int DumpCustom::add_variable(char *id) id_variable = (char **) memory->srealloc(id_variable,(nvariable+1)*sizeof(char *), - "dump:id_variable"); + "dsrealloc(id_custom,(ncustom+1)*sizeof(char *),"dump:id_custom"); - flag_custom = (int *) - memory->srealloc(flag_custom,(ncustom+1)*sizeof(int),"dump:flag_custom"); + + delete [] custom; + custom = new int[ncustom+1]; + delete [] custom_flag; + custom_flag = new int[ncustom+1]; int n = strlen(id) + 1; id_custom[ncustom] = new char[n]; strcpy(id_custom[ncustom],id); - flag_custom[ncustom] = flag; ncustom++; return ncustom-1; @@ -1777,7 +1821,7 @@ int DumpCustom::modify_param(int narg, char **arg) if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); if (strncmp(arg[1],"c_",2) != 0) error->all(FLERR,"Illegal dump_modify command"); - if (refreshflag) error->all(FLERR,"Dump modify can only have one refresh"); + if (refreshflag) error->all(FLERR,"Dump_modify can only have one refresh"); refreshflag = 1; int n = strlen(arg[1]); @@ -1914,28 +1958,29 @@ int DumpCustom::modify_param(int narg, char **arg) char *ptr = strchr(suffix,'['); if (ptr) { if (suffix[strlen(suffix)-1] != ']') - error->all(FLERR,"Invalid attribute in dump modify command"); - argindex[nfield+nthresh] = atoi(ptr+1); + error->all(FLERR,"Invalid attribute in dump_modify command"); + suffix[strlen(suffix)-1] = '\0'; + argindex[nfield+nthresh] = utils::inumeric(FLERR,ptr+1,true,lmp); *ptr = '\0'; } else argindex[nfield+nthresh] = 0; n = modify->find_compute(suffix); - if (n < 0) error->all(FLERR,"Could not find dump modify compute ID"); + if (n < 0) error->all(FLERR,"Could not find dump_modify compute ID"); if (modify->compute[n]->peratom_flag == 0) error->all(FLERR, - "Dump modify compute ID does not compute per-atom info"); + "Dump_modify compute ID does not compute per-atom info"); if (argindex[nfield+nthresh] == 0 && modify->compute[n]->size_peratom_cols > 0) error->all(FLERR, - "Dump modify compute ID does not compute per-atom vector"); + "Dump_modify compute ID does not compute per-atom vector"); if (argindex[nfield+nthresh] > 0 && modify->compute[n]->size_peratom_cols == 0) error->all(FLERR, - "Dump modify compute ID does not compute per-atom array"); + "Dump_modify compute ID does not compute per-atom array"); if (argindex[nfield+nthresh] > 0 && argindex[nfield+nthresh] > modify->compute[n]->size_peratom_cols) - error->all(FLERR,"Dump modify compute ID vector is not large enough"); + error->all(FLERR,"Dump_modify compute ID vector is not large enough"); field2index[nfield+nthresh] = add_compute(suffix); delete [] suffix; @@ -1955,25 +2000,26 @@ int DumpCustom::modify_param(int narg, char **arg) char *ptr = strchr(suffix,'['); if (ptr) { if (suffix[strlen(suffix)-1] != ']') - error->all(FLERR,"Invalid attribute in dump modify command"); - argindex[nfield+nthresh] = atoi(ptr+1); + error->all(FLERR,"Invalid attribute in dump_modify command"); + suffix[strlen(suffix)-1] = '\0'; + argindex[nfield+nthresh] = utils::inumeric(FLERR,ptr+1,true,lmp); *ptr = '\0'; } else argindex[nfield+nthresh] = 0; n = modify->find_fix(suffix); - if (n < 0) error->all(FLERR,"Could not find dump modify fix ID"); + if (n < 0) error->all(FLERR,"Could not find dump_modify fix ID"); if (modify->fix[n]->peratom_flag == 0) - error->all(FLERR,"Dump modify fix ID does not compute per-atom info"); + error->all(FLERR,"Dump_modify fix ID does not compute per-atom info"); if (argindex[nfield+nthresh] == 0 && modify->fix[n]->size_peratom_cols > 0) - error->all(FLERR,"Dump modify fix ID does not compute per-atom vector"); + error->all(FLERR,"Dump_modify fix ID does not compute per-atom vector"); if (argindex[nfield+nthresh] > 0 && modify->fix[n]->size_peratom_cols == 0) - error->all(FLERR,"Dump modify fix ID does not compute per-atom array"); + error->all(FLERR,"Dump_modify fix ID does not compute per-atom array"); if (argindex[nfield+nthresh] > 0 && argindex[nfield+nthresh] > modify->fix[n]->size_peratom_cols) - error->all(FLERR,"Dump modify fix ID vector is not large enough"); + error->all(FLERR,"Dump_modify fix ID vector is not large enough"); field2index[nfield+nthresh] = add_fix(suffix); delete [] suffix; @@ -1992,18 +2038,23 @@ int DumpCustom::modify_param(int narg, char **arg) argindex[nfield+nthresh] = 0; n = input->variable->find(suffix); - if (n < 0) error->all(FLERR,"Could not find dump modify variable name"); + if (n < 0) error->all(FLERR,"Could not find dump_modify variable name"); if (input->variable->atomstyle(n) == 0) - error->all(FLERR,"Dump modify variable is not atom-style variable"); + error->all(FLERR,"Dump_modify variable is not atom-style variable"); field2index[nfield+nthresh] = add_variable(suffix); delete [] suffix; - // custom per atom floating point value = d_ID + // custom per-atom vector = i_ID or d_ID // must grow field2index and argindex arrays, since access is beyond nfield - } else if (strncmp(arg[1],"d_",2) == 0) { - thresh_array[nthresh] = DNAME; + } else if (strncmp(arg[1],"i_",2) == 0 || + strncmp(arg[1],"d_",2) == 0) { + int which = 0; + if (arg[1][0] == 'd') which = 1; + + if (!which) thresh_array[nthresh] = IVEC; + else thresh_array[nthresh] = DVEC; memory->grow(field2index,nfield+nthresh+1,"dump:field2index"); memory->grow(argindex,nfield+nthresh+1,"dump:argindex"); int n = strlen(arg[1]); @@ -2011,34 +2062,51 @@ int DumpCustom::modify_param(int narg, char **arg) strcpy(suffix,&arg[1][2]); argindex[nfield+nthresh] = 0; - int tmp = -1; - n = atom->find_custom(suffix,tmp); - if ((n < 0) || (tmp != 1)) - error->all(FLERR,"Could not find dump modify " - "custom atom floating point property ID"); - - field2index[nfield+nthresh] = add_custom(suffix,1); + int flag,cols; + n = atom->find_custom(suffix,flag,cols); + if ((!which && (n < 0 || flag || cols)) || + (which && (n < 0 || !flag || cols))) + error->all(FLERR,"Could not find dump_modify per-atom custom vector"); + field2index[nfield+nthresh] = add_custom(suffix); delete [] suffix; - // custom per atom integer value = i_ID + // custom per-atom array = i2_ID or d2_ID, must include bracketed index // must grow field2index and argindex arrays, since access is beyond nfield - } else if (strncmp(arg[1],"i_",2) == 0) { - thresh_array[nthresh] = INAME; + } else if (strncmp(arg[1],"i2_",3) == 0 || + strncmp(arg[1],"d2_",3) == 0) { + int which = 0; + if (arg[1][0] == 'd') which = 1; + + if (!which) thresh_array[nthresh] = IARRAY; + else thresh_array[nthresh] = DARRAY; memory->grow(field2index,nfield+nthresh+1,"dump:field2index"); memory->grow(argindex,nfield+nthresh+1,"dump:argindex"); + int n = strlen(arg[1]); char *suffix = new char[n]; - strcpy(suffix,&arg[1][2]); - argindex[nfield+nthresh] = 0; + strcpy(suffix,&arg[1][3]); - int tmp = -1; - n = atom->find_custom(suffix,tmp); - if ((n < 0) || (tmp != 0)) - error->all(FLERR,"Could not find dump modify " - "custom atom integer property ID"); + char *ptr = strchr(suffix,'['); + if (ptr) { + if (suffix[strlen(suffix)-1] != ']') + error->all(FLERR,"Invalid attribute in dump custom command"); + suffix[strlen(suffix)-1] = '\0'; + argindex[nfield+nthresh] = utils::inumeric(FLERR,ptr+1,true,lmp); + *ptr = '\0'; + } else error->all(FLERR,"Dump_modify per-atom custom array is not indexed"); - field2index[nfield+nthresh] = add_custom(suffix,0); + int flag,cols; + n = atom->find_custom(suffix,flag,cols); + + if ((!which && (n < 0 || flag || !cols)) || + (which && (n < 0 || !flag || !cols))) + error->all(FLERR,"Could not find dump_modify per-atom custom array"); + if (argindex[nfield+nthresh] <= 0 || argindex[nfield+nthresh] > cols) + error->all(FLERR, + "Dump_modify per-atom custom array is accessed out-of-range"); + + field2index[nfield+nthresh] = add_custom(suffix); delete [] suffix; } else error->all(FLERR,"Invalid dump_modify thresh attribute"); @@ -2165,27 +2233,36 @@ void DumpCustom::pack_variable(int n) void DumpCustom::pack_custom(int n) { - - int index = field2index[n]; - - if (flag_custom[index] == 0) { // integer - int iwhich,tmp; - iwhich = atom->find_custom(id_custom[index],tmp); - + int flag = custom_flag[field2index[n]]; + int iwhich = custom[field2index[n]]; + int index = argindex[n]; + + if (flag == IVEC) { int *ivector = atom->ivector[iwhich]; for (int i = 0; i < nchoose; i++) { buf[n] = ivector[clist[i]]; n += size_one; } - } else if (flag_custom[index] == 1) { // double - int iwhich,tmp; - iwhich = atom->find_custom(id_custom[index],tmp); - + } else if (flag == DVEC) { double *dvector = atom->dvector[iwhich]; for (int i = 0; i < nchoose; i++) { buf[n] = dvector[clist[i]]; n += size_one; } + } else if (flag == IARRAY) { + index--; + int **iarray = atom->iarray[iwhich]; + for (int i = 0; i < nchoose; i++) { + buf[n] = iarray[clist[i]][index]; + n += size_one; + } + } else if (flag == DARRAY) { + index--; + double **darray = atom->darray[iwhich]; + for (int i = 0; i < nchoose; i++) { + buf[n] = darray[clist[i]][index]; + n += size_one; + } } } diff --git a/src/dump_custom.h b/src/dump_custom.h index 0f63eac8de..d800acf525 100644 --- a/src/dump_custom.h +++ b/src/dump_custom.h @@ -70,29 +70,30 @@ class DumpCustom : public Dump { int nfield; // # of keywords listed by user int ioptional; // index of start of optional args - int *field2index; // which compute,fix,variable calcs this field - int *argindex; // index into compute,fix scalar_atom,vector_atom - // 0 for scalar_atom, 1-N for vector_atom values + int *field2index; // which compute,fix,variable,custom calcs this field + int *argindex; // index into compute,fix,custom per-atom data + // 0 for per-atom vector, 1-N for cols of per-atom array - int ncompute; // # of Compute objects used by dump + int ncompute; // # of Computes accessed by dump char **id_compute; // their IDs - class Compute **compute; // list of ptrs to the Compute objects + class Compute **compute; // list of ptrs to the Computes - int nfix; // # of Fix objects used by dump + int nfix; // # of Fixes used by dump char **id_fix; // their IDs - class Fix **fix; // list of ptrs to the Fix objects + class Fix **fix; // list of ptrs to the Fixes int nvariable; // # of Variables used by dump char **id_variable; // their names - int *variable; // list of indices for the Variables + int *variable; // list of Variable indices in Variable class double **vbuf; // local storage for variable evaluation - int ncustom; // # of custom atom properties + int ncustom; // # of Custom atom properties used by dump char **id_custom; // their names - int *flag_custom; // their data type + int *custom; // list of Custom indices in Atom class + int *custom_flag; // list of IVEC,DVEC,IARRAY,DARRAY styles int ntypes; // # of atom types - char **typenames; // array of element names for each type + char **typenames; // array of element names for each type // private methods @@ -108,7 +109,7 @@ class DumpCustom : public Dump { int add_compute(char *); int add_fix(char *); int add_variable(char *); - int add_custom(char *, int); + int add_custom(char *); virtual int modify_param(int, char **); void header_format_binary(); diff --git a/src/fix_group.cpp b/src/fix_group.cpp index d2eea9f781..17f1d3c60b 100644 --- a/src/fix_group.cpp +++ b/src/fix_group.cpp @@ -64,6 +64,7 @@ idregion(NULL), idvar(NULL), idprop(NULL) idregion = new char[n]; strcpy(idregion,arg[iarg+1]); iarg += 2; + } else if (strcmp(arg[iarg],"var") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal group command"); if (input->variable->find(arg[iarg+1]) < 0) @@ -74,16 +75,21 @@ idregion(NULL), idvar(NULL), idprop(NULL) idvar = new char[n]; strcpy(idvar,arg[iarg+1]); iarg += 2; + } else if (strcmp(arg[iarg],"property") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal group command"); - if (atom->find_custom(arg[iarg+1],typeflag) < 0) - error->all(FLERR,"Per atom property for group dynamic does not exist"); + if (iarg+2 > narg) error->all(FLERR,"Illegal group command"); + int flag,cols; + iprop = atom->find_custom(arg[iarg+1],flag,cols); + if (iprop < 1 || cols) + error->all(FLERR,"Custom per-atom vector for group dynamic " + "does not exist"); propflag = 1; delete [] idprop; int n = strlen(arg[iarg+1]) + 1; idprop = new char[n]; strcpy(idprop,arg[iarg+1]); iarg += 2; + } else if (strcmp(arg[iarg],"every") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal group command"); nevery = force->inumeric(FLERR,arg[iarg+1]); @@ -125,7 +131,7 @@ void FixGroup::init() if (strstr(update->integrate_style,"respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; - // set current indices for region and variable + // set current indices for region and variable and custom property if (regionflag) { iregion = domain->find_region(idregion); @@ -143,9 +149,10 @@ void FixGroup::init() } if (propflag) { - iprop = atom->find_custom(idprop,typeflag); - if (iprop < 0) - error->all(FLERR,"Per-atom property for group dynamic does not exist"); + int cols; + iprop = atom->find_custom(idprop,proptype,cols); + if (iprop < 0 || cols) + error->all(FLERR,"Group dynamic command custom property vector does not exist"); } // warn if any FixGroup is not at tail end of all post_integrate fixes @@ -222,11 +229,10 @@ void FixGroup::set_group() update->post_integrate = 0; } - // invoke per-atom property if defined + // set ptr to custom atom vector - if (propflag && !typeflag) ivector = atom->ivector[iprop]; //check nlocal > 0? - - if (propflag && typeflag) dvector = atom->dvector[iprop]; //check nlocal > 0? + if (propflag && !proptype) ivector = atom->ivector[iprop]; + if (propflag && proptype) dvector = atom->dvector[iprop]; // update region in case it has a variable dependence or is dynamic @@ -246,8 +252,10 @@ void FixGroup::set_group() inflag = 1; if (regionflag && !region->match(x[i][0],x[i][1],x[i][2])) inflag = 0; if (varflag && var[i] == 0.0) inflag = 0; - if (propflag && !typeflag && ivector[i] == 0) inflag = 0; - if (propflag && typeflag && dvector[i] == 0) inflag = 0; + if (propflag) { + if (!proptype && ivector[i] == 0) inflag = 0; + if (proptype && dvector[i] == 0.0) inflag = 0; + } } else inflag = 0; if (inflag) mask[i] |= gbit; diff --git a/src/fix_group.h b/src/fix_group.h index f3fecac316..56e4ade06d 100644 --- a/src/fix_group.h +++ b/src/fix_group.h @@ -37,7 +37,7 @@ class FixGroup : public Fix { private: int gbit,gbitinverse; - int regionflag,varflag,propflag,typeflag; + int regionflag,varflag,propflag,proptype; int iregion,ivar,iprop; char *idregion,*idvar,*idprop; class Region *region; diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 374d0069fd..2b004a0ba8 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; using namespace FixConst; -enum{MOLECULE,CHARGE,RMASS,INTEGER,DOUBLE}; +enum{MOLECULE,CHARGE,RMASS,IVEC,DVEC,IARRAY,DARRAY}; /* ---------------------------------------------------------------------- */ @@ -40,6 +40,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) : int iarg = 3; nvalue = narg-iarg; style = new int[nvalue]; + cols = new int[nvalue]; index = new int[nvalue]; molecule_flag = 0; @@ -47,6 +48,8 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) : rmass_flag = 0; nvalue = 0; + values_peratom = 0; + while (iarg < narg) { if (strcmp(arg[iarg],"mol") == 0) { if (atom->molecule_flag) @@ -55,8 +58,11 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) : if (molecule_flag) error->all(FLERR,"Fix property/atom cannot specify mol twice"); style[nvalue] = MOLECULE; + cols[nvalue] = 0; atom->molecule_flag = molecule_flag = 1; + values_peratom++; nvalue++; + iarg++; } else if (strcmp(arg[iarg],"q") == 0) { if (atom->q_flag) error->all(FLERR,"Fix property/atom q when atom_style " @@ -64,8 +70,11 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) : if (q_flag) error->all(FLERR,"Fix property/atom cannot specify q twice"); style[nvalue] = CHARGE; + cols[nvalue] = 0; atom->q_flag = q_flag = 1; + values_peratom++; nvalue++; + iarg++; } else if (strcmp(arg[iarg],"rmass") == 0) { if (atom->rmass_flag) error->all(FLERR,"Fix property/atom rmass when atom_style " @@ -73,27 +82,45 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) : if (rmass_flag) error->all(FLERR,"Fix property/atom cannot specify rmass twice"); style[nvalue] = RMASS; + cols[nvalue] = 0; atom->rmass_flag = rmass_flag = 1; + values_peratom++; nvalue++; - } else if (strstr(arg[iarg],"i_") == arg[iarg]) { - style[nvalue] = INTEGER; - int tmp; - index[nvalue] = atom->find_custom(&arg[iarg][2],tmp); + iarg++; + } else if (strstr(arg[iarg],"i_") == arg[iarg] || + strstr(arg[iarg],"d_") == arg[iarg]) { + int which = 0; + if (arg[iarg][0] == 'd') which = 1; + if (which == 0) style[nvalue] = IVEC; + else style[nvalue] = DVEC; + int tmp1,tmp2; + index[nvalue] = atom->find_custom(&arg[iarg][2],tmp1,tmp2); if (index[nvalue] >= 0) error->all(FLERR,"Fix property/atom vector name already exists"); - index[nvalue] = atom->add_custom(&arg[iarg][2],0); + cols[nvalue] = 0; + index[nvalue] = atom->add_custom(&arg[iarg][2],which,cols[nvalue]); + values_peratom++; nvalue++; - } else if (strstr(arg[iarg],"d_") == arg[iarg]) { - style[nvalue] = DOUBLE; - int tmp; - index[nvalue] = atom->find_custom(&arg[iarg][2],tmp); + iarg++; + } else if (strstr(arg[iarg],"i2_") == arg[iarg] || + strstr(arg[iarg],"d2_") == arg[iarg]) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix property/atom command"); + int which = 0; + if (arg[iarg][0] == 'd') which = 1; + if (which == 0) style[nvalue] = IARRAY; + else style[nvalue] = DARRAY; + int tmp1,tmp2; + index[nvalue] = atom->find_custom(&arg[iarg][3],tmp1,tmp2); if (index[nvalue] >= 0) - error->all(FLERR,"Fix property/atom vector name already exists"); - index[nvalue] = atom->add_custom(&arg[iarg][2],1); + error->all(FLERR,"Fix property/atom array name already exists"); + cols[nvalue] = utils::inumeric(FLERR,arg[iarg+1],true,lmp); + if (cols[nvalue] < 1) + error->all(FLERR,"Invalid array columns in fix property/atom"); + index[nvalue] = atom->add_custom(&arg[iarg][3],which,cols[nvalue]); + values_peratom += cols[nvalue]; nvalue++; + iarg += 2; } else break; - - iarg++; } // optional args @@ -109,7 +136,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) : } else error->all(FLERR,"Illegal fix property/atom command"); } - if (border) comm_border = nvalue; + if (border) comm_border = values_peratom; // warn if mol or charge keyword used without ghost yes @@ -134,8 +161,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) : // register with Atom class nmax_old = 0; - if (!lmp->kokkos) - grow_arrays(atom->nmax); + if (!lmp->kokkos) grow_arrays(atom->nmax); atom->add_callback(0); atom->add_callback(1); if (border) atom->add_callback(2); @@ -154,27 +180,32 @@ FixPropertyAtom::~FixPropertyAtom() // deallocate per-atom vectors in Atom class // set ptrs to NULL, so they no longer exist for Atom class - for (int m = 0; m < nvalue; m++) { - if (style[m] == MOLECULE) { + for (int nv = 0; nv < nvalue; nv++) { + if (style[nv] == MOLECULE) { atom->molecule_flag = 0; memory->destroy(atom->molecule); atom->molecule = NULL; - } else if (style[m] == CHARGE) { + } else if (style[nv] == CHARGE) { atom->q_flag = 0; memory->destroy(atom->q); atom->q = NULL; - } else if (style[m] == RMASS) { + } else if (style[nv] == RMASS) { atom->rmass_flag = 0; memory->destroy(atom->rmass); atom->rmass = NULL; - } else if (style[m] == INTEGER) { - atom->remove_custom(0,index[m]); - } else if (style[m] == DOUBLE) { - atom->remove_custom(1,index[m]); + } else if (style[nv] == IVEC) { + atom->remove_custom(index[nv],0,cols[nv]); + } else if (style[nv] == DVEC) { + atom->remove_custom(index[nv],1,cols[nv]); + } else if (style[nv] == IARRAY) { + atom->remove_custom(index[nv],0,cols[nv]); + } else if (style[nv] == DARRAY) { + atom->remove_custom(index[nv],1,cols[nv]); } } delete [] style; + delete [] cols; delete [] index; delete [] astyle; } @@ -206,7 +237,7 @@ void FixPropertyAtom::init() void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, tagint id_offset) { - int j,m; + int j,k,m,iword,ncol,nv; tagint itag; char *next; @@ -222,7 +253,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, int nwords = utils::trim_and_count_words(buf); *next = '\n'; - if (nwords != nvalue+1) + if (nwords != values_peratom+1) error->all(FLERR,fmt::format("Incorrect {} format in data file",keyword)); char **values = new char*[nwords]; @@ -254,16 +285,27 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, "data file",itag, keyword)); // assign words in line to per-atom vectors - + // iword = position in vector of words + if ((m = atom->map(itag)) >= 0) { - for (j = 0; j < nvalue; j++) { - if (style[j] == MOLECULE) atom->molecule[m] = ATOTAGINT(values[j+1]); - else if (style[j] == CHARGE) atom->q[m] = atof(values[j+1]); - else if (style[j] == RMASS) atom->rmass[m] = atof(values[j+1]); - else if (style[j] == INTEGER) - atom->ivector[index[j]][m] = atoi(values[j+1]); - else if (style[j] == DOUBLE) - atom->dvector[index[j]][m] = atof(values[j+1]); + iword = 1; + for (nv = 0; nv < nvalue; nv++) { + if (style[nv] == MOLECULE) atom->molecule[m] = ATOTAGINT(values[iword++]); + else if (style[nv] == CHARGE) atom->q[m] = atof(values[iword++]); + else if (style[nv] == RMASS) atom->rmass[m] = atof(values[iword++]); + else if (style[nv] == IVEC) + atom->ivector[index[nv]][m] = atoi(values[iword++]); + else if (style[nv] == DVEC) + atom->dvector[index[nv]][m] = atof(values[iword++]); + else if (style[nv] == IARRAY) { + ncol = cols[nv]; + for (k = 0; k < ncol; k++) + atom->iarray[index[nv]][m][k] = atoi(values[iword++]); + } else if (style[nv] == DARRAY) { + ncol = cols[nv]; + for (k = 0; k < ncol; k++) + atom->darray[index[nv]][m][k] = atof(values[iword++]); + } } } @@ -291,13 +333,13 @@ bigint FixPropertyAtom::read_data_skip_lines(char * /*keyword*/) return size I own for Mth data section # of data sections = 1 for this fix nx = # of local atoms - ny = columns = tag + nvalues + ny = columns = tag + values_peratom ------------------------------------------------------------------------- */ void FixPropertyAtom::write_data_section_size(int /*mth*/, int &nx, int &ny) { nx = atom->nlocal; - ny = nvalue + 1; + ny = values_peratom + 1; } /* ---------------------------------------------------------------------- @@ -307,7 +349,7 @@ void FixPropertyAtom::write_data_section_size(int /*mth*/, int &nx, int &ny) void FixPropertyAtom::write_data_section_pack(int /*mth*/, double **buf) { - int i; + int i,k,ncol; // 1st column = atom tag // rest of columns = per-atom values @@ -317,23 +359,42 @@ void FixPropertyAtom::write_data_section_pack(int /*mth*/, double **buf) for (i = 0; i < nlocal; i++) buf[i][0] = ubuf(tag[i]).d; - for (int m = 0; m < nvalue; m++) { - int mp1 = m+1; - if (style[m] == MOLECULE) { + int icol = 1; + for (int nv = 0; nv < nvalue; nv++) { + if (style[nv] == MOLECULE) { tagint *molecule = atom->molecule; - for (i = 0; i < nlocal; i++) buf[i][mp1] = ubuf(molecule[i]).d; - } else if (style[m] == CHARGE) { + for (i = 0; i < nlocal; i++) buf[i][icol] = ubuf(molecule[i]).d; + icol++; + } else if (style[nv] == CHARGE) { double *q = atom->q; - for (i = 0; i < nlocal; i++) buf[i][mp1] = q[i]; - } else if (style[m] == RMASS) { + for (i = 0; i < nlocal; i++) buf[i][icol] = q[i]; + icol++; + } else if (style[nv] == RMASS) { double *rmass = atom->rmass; - for (i = 0; i < nlocal; i++) buf[i][mp1] = rmass[i]; - } else if (style[m] == INTEGER) { - int *ivec = atom->ivector[index[m]]; - for (i = 0; i < nlocal; i++) buf[i][mp1] = ubuf(ivec[i]).d; - } else if (style[m] == DOUBLE) { - double *dvec = atom->dvector[index[m]]; - for (i = 0; i < nlocal; i++) buf[i][mp1] = dvec[i]; + for (i = 0; i < nlocal; i++) buf[i][icol] = rmass[i]; + icol++; + } else if (style[nv] == IVEC) { + int *ivec = atom->ivector[index[nv]]; + for (i = 0; i < nlocal; i++) buf[i][icol] = ubuf(ivec[i]).d; + icol++; + } else if (style[nv] == DVEC) { + double *dvec = atom->dvector[index[nv]]; + for (i = 0; i < nlocal; i++) buf[i][icol] = dvec[i]; + icol++; + } else if (style[nv] == IARRAY) { + int **iarray = atom->iarray[index[nv]]; + ncol = cols[nv]; + for (i = 0; i < nlocal; i++) + for (k = 0; k < ncol; k++) + buf[i][icol+k] = ubuf(iarray[i][k]).d; + icol += ncol; + } else if (style[nv] == DARRAY) { + double **darray = atom->darray[index[nv]]; + ncol = cols[nv]; + for (i = 0; i < nlocal; i++) + for (k = 0; k < ncol; k++) + buf[i][icol+k] = ubuf(darray[i][k]).d; + icol += ncol; } } } @@ -361,16 +422,33 @@ void FixPropertyAtom::write_data_section_keyword(int /*mth*/, FILE *fp) void FixPropertyAtom::write_data_section(int /*mth*/, FILE *fp, int n, double **buf, int /*index*/) { - int m; + int k,icol,ncol,nv; for (int i = 0; i < n; i++) { fprintf(fp,TAGINT_FORMAT,(tagint) ubuf(buf[i][0]).i); - for (m = 0; m < nvalue; m++) { - if (style[m] == MOLECULE) - fprintf(fp," " TAGINT_FORMAT,(tagint) ubuf(buf[i][m+1]).i); - else if (style[m] == INTEGER) - fprintf(fp," %d",(int) ubuf(buf[i][m+1]).i); - else fprintf(fp," %g",buf[i][m+1]); + icol = 1; + for (nv = 0; nv < nvalue; nv++) { + if (style[nv] == MOLECULE) + fprintf(fp," " TAGINT_FORMAT,(tagint) ubuf(buf[i][icol++]).i); + else if (style[nv] == CHARGE) + fprintf(fp," %g",buf[i][icol++]); + else if (style[nv] == RMASS) + fprintf(fp," %g",buf[i][icol++]); + else if (style[nv] == IVEC) + fprintf(fp," %d",(int) ubuf(buf[i][icol++]).i); + else if (style[nv] == DVEC) + fprintf(fp," %g",buf[i][icol++]); + else if (style[nv] == IARRAY) { + ncol = cols[nv]; + for (k = 0; k < ncol; k++) + fprintf(fp," %d",(int) ubuf(buf[i][icol+k]).i); + icol += ncol; + } else if (style[nv] == DARRAY) { + ncol = cols[nv]; + for (k = 0; k < ncol; k++) + fprintf(fp," %g",buf[i][icol+k]); + icol += ncol; + } } fprintf(fp,"\n"); } @@ -387,42 +465,52 @@ double FixPropertyAtom::memory_usage() if (style[m] == MOLECULE) bytes = atom->nmax * sizeof(tagint); else if (style[m] == CHARGE) bytes = atom->nmax * sizeof(double); else if (style[m] == RMASS) bytes = atom->nmax * sizeof(double); - else if (style[m] == INTEGER) bytes = atom->nmax * sizeof(int); - else if (style[m] == DOUBLE) bytes = atom->nmax * sizeof(double); + else if (style[m] == IVEC) bytes = atom->nmax * sizeof(int); + else if (style[m] == DVEC) bytes = atom->nmax * sizeof(double); + else if (style[m] == IARRAY) bytes = atom->nmax * cols[m] * sizeof(int); + else if (style[m] == DARRAY) bytes = atom->nmax * cols[m] * sizeof(double); } return bytes; } /* ---------------------------------------------------------------------- allocate atom-based arrays - initialize new values to 0, - since AtomVec class won't do it as atoms are added, - e.g. in create_atom() or data_atom() + also initialize new values to 0 + since AtomVec class won't do it as atoms are added, + e.g. in create_atom() or data_atom() ------------------------------------------------------------------------- */ void FixPropertyAtom::grow_arrays(int nmax) { - for (int m = 0; m < nvalue; m++) { - if (style[m] == MOLECULE) { + for (int nv = 0; nv < nvalue; nv++) { + if (style[nv] == MOLECULE) { memory->grow(atom->molecule,nmax,"atom:molecule"); size_t nbytes = (nmax-nmax_old) * sizeof(tagint); memset(&atom->molecule[nmax_old],0,nbytes); - } else if (style[m] == CHARGE) { + } else if (style[nv] == CHARGE) { memory->grow(atom->q,nmax,"atom:q"); size_t nbytes = (nmax-nmax_old) * sizeof(double); memset(&atom->q[nmax_old],0,nbytes); - } else if (style[m] == RMASS) { + } else if (style[nv] == RMASS) { memory->grow(atom->rmass,nmax,"atom:rmass"); size_t nbytes = (nmax-nmax_old) * sizeof(double); memset(&atom->rmass[nmax_old],0,nbytes); - } else if (style[m] == INTEGER) { - memory->grow(atom->ivector[index[m]],nmax,"atom:ivector"); + } else if (style[nv] == IVEC) { + memory->grow(atom->ivector[index[nv]],nmax,"atom:ivector"); size_t nbytes = (nmax-nmax_old) * sizeof(int); - memset(&atom->ivector[index[m]][nmax_old],0,nbytes); - } else if (style[m] == DOUBLE) { - memory->grow(atom->dvector[index[m]],nmax,"atom:dvector"); + memset(&atom->ivector[index[nv]][nmax_old],0,nbytes); + } else if (style[nv] == DVEC) { + memory->grow(atom->dvector[index[nv]],nmax,"atom:dvector"); size_t nbytes = (nmax-nmax_old) * sizeof(double); - memset(&atom->dvector[index[m]][nmax_old],0,nbytes); + memset(&atom->dvector[index[nv]][nmax_old],0,nbytes); + } else if (style[nv] == IARRAY) { + memory->grow(atom->iarray[index[nv]],nmax,cols[nv],"atom:iarray"); + size_t nbytes = (nmax-nmax_old) * cols[nv] * sizeof(int); + if (nbytes) memset(&atom->iarray[index[nv]][nmax_old][0],0,nbytes); + } else if (style[nv] == DARRAY) { + memory->grow(atom->darray[index[nv]],nmax,cols[nv],"atom:darray"); + size_t nbytes = (nmax-nmax_old) * cols[nv] * sizeof(double); + if (nbytes) memset(&atom->darray[index[nv]][nmax_old][0],0,nbytes); } } @@ -435,17 +523,28 @@ void FixPropertyAtom::grow_arrays(int nmax) void FixPropertyAtom::copy_arrays(int i, int j, int /*delflag*/) { - for (int m = 0; m < nvalue; m++) { - if (style[m] == MOLECULE) + int k,ncol; + + for (int nv = 0; nv < nvalue; nv++) { + if (style[nv] == MOLECULE) atom->molecule[j] = atom->molecule[i]; - else if (style[m] == CHARGE) + else if (style[nv] == CHARGE) atom->q[j] = atom->q[i]; - else if (style[m] == RMASS) + else if (style[nv] == RMASS) atom->rmass[j] = atom->rmass[i]; - else if (style[m] == INTEGER) - atom->ivector[index[m]][j] = atom->ivector[index[m]][i]; - else if (style[m] == DOUBLE) - atom->dvector[index[m]][j] = atom->dvector[index[m]][i]; + else if (style[nv] == IVEC) + atom->ivector[index[nv]][j] = atom->ivector[index[nv]][i]; + else if (style[nv] == DVEC) + atom->dvector[index[nv]][j] = atom->dvector[index[nv]][i]; + else if (style[nv] == IARRAY) { + ncol = cols[nv]; + for (k = 0; k < ncol; k++) + atom->iarray[index[nv]][j][k] = atom->iarray[index[nv]][i][k]; + } else if (style[nv] == DARRAY) { + ncol = cols[nv]; + for (k = 0; k < ncol; k++) + atom->darray[index[nv]][j][k] = atom->darray[index[nv]][i][k]; + } } } @@ -455,40 +554,56 @@ void FixPropertyAtom::copy_arrays(int i, int j, int /*delflag*/) int FixPropertyAtom::pack_border(int n, int *list, double *buf) { - int i,j,k; + int i,j,k,ncol; int m = 0; - for (k = 0; k < nvalue; k++) { - if (style[k] == MOLECULE) { + for (int nv = 0; nv < nvalue; nv++) { + if (style[nv] == MOLECULE) { tagint *molecule = atom->molecule; for (i = 0; i < n; i++) { j = list[i]; buf[m++] = ubuf(molecule[j]).d; } - } else if (style[k] == CHARGE) { + } else if (style[nv] == CHARGE) { double *q = atom->q; for (i = 0; i < n; i++) { j = list[i]; buf[m++] = q[j]; } - } else if (style[k] == RMASS) { + } else if (style[nv] == RMASS) { double *rmass = atom->rmass; for (i = 0; i < n; i++) { j = list[i]; buf[m++] = rmass[j]; } - } else if (style[k] == INTEGER) { - int *ivector = atom->ivector[index[k]]; + } else if (style[nv] == IVEC) { + int *ivector = atom->ivector[index[nv]]; for (i = 0; i < n; i++) { j = list[i]; buf[m++] = ubuf(ivector[j]).d; } - } else if (style[k] == DOUBLE) { - double *dvector = atom->dvector[index[k]]; + } else if (style[nv] == DVEC) { + double *dvector = atom->dvector[index[nv]]; for (i = 0; i < n; i++) { j = list[i]; buf[m++] = dvector[j]; } + } else if (style[nv] == IARRAY) { + int **iarray = atom->iarray[index[nv]]; + ncol = cols[nv]; + for (i = 0; i < n; i++) { + j = list[i]; + for (k = 0; k < ncol; k++) + buf[m++] = ubuf(iarray[j][k]).d; + } + } else if (style[nv] == DARRAY) { + double **darray = atom->darray[index[nv]]; + ncol = cols[nv]; + for (i = 0; i < n; i++) { + j = list[i]; + for (k = 0; k < ncol; k++) + buf[m++] = darray[j][k]; + } } } @@ -501,35 +616,49 @@ int FixPropertyAtom::pack_border(int n, int *list, double *buf) int FixPropertyAtom::unpack_border(int n, int first, double *buf) { - int i,k,last; + int i,k,last,ncol; int m = 0; - for (k = 0; k < nvalue; k++) { - if (style[k] == MOLECULE) { + for (int nv = 0; nv < nvalue; nv++) { + if (style[nv] == MOLECULE) { tagint *molecule = atom->molecule; last = first + n; for (i = first; i < last; i++) molecule[i] = (tagint) ubuf(buf[m++]).i; - } else if (style[k] == CHARGE) { + } else if (style[nv] == CHARGE) { double *q = atom->q; last = first + n; for (i = first; i < last; i++) q[i] = buf[m++]; - } else if (style[k] == RMASS) { + } else if (style[nv] == RMASS) { double *rmass = atom->rmass; last = first + n; for (i = first; i < last; i++) rmass[i] = buf[m++]; - } else if (style[k] == INTEGER) { - int *ivector = atom->ivector[index[k]]; + } else if (style[nv] == IVEC) { + int *ivector = atom->ivector[index[nv]]; last = first + n; for (i = first; i < last; i++) ivector[i] = (int) ubuf(buf[m++]).i; - } else if (style[k] == DOUBLE) { - double *dvector = atom->dvector[index[k]]; + } else if (style[nv] == DVEC) { + double *dvector = atom->dvector[index[nv]]; last = first + n; for (i = first; i < last; i++) dvector[i] = buf[m++]; + } else if (style[nv] == IARRAY) { + int **iarray = atom->iarray[index[nv]]; + ncol = cols[nv]; + last = first + n; + for (i = first; i < last; i++) + for (k = 0; k < ncol; k++) + iarray[i][k] = (int) ubuf(buf[m++]).i; + } else if (style[nv] == DARRAY) { + double **darray = atom->darray[index[nv]]; + ncol = cols[nv]; + last = first + n; + for (i = first; i < last; i++) + for (k = 0; k < ncol; k++) + darray[i][k] = buf[m++]; } } @@ -542,14 +671,27 @@ int FixPropertyAtom::unpack_border(int n, int first, double *buf) int FixPropertyAtom::pack_exchange(int i, double *buf) { - for (int m = 0; m < nvalue; m++) { - if (style[m] == MOLECULE) buf[m] = ubuf(atom->molecule[i]).d; - else if (style[m] == CHARGE) buf[m] = atom->q[i]; - else if (style[m] == RMASS) buf[m] = atom->rmass[i]; - else if (style[m] == INTEGER) buf[m] = ubuf(atom->ivector[index[m]][i]).d; - else if (style[m] == DOUBLE) buf[m] = atom->dvector[index[m]][i]; + int k,ncol; + + int m = 0; + for (int nv = 0; nv < nvalue; nv++) { + if (style[nv] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d; + else if (style[nv] == CHARGE) buf[m++] = atom->q[i]; + else if (style[nv] == RMASS) buf[m++] = atom->rmass[i]; + else if (style[nv] == IVEC) buf[m++] = ubuf(atom->ivector[index[nv]][i]).d; + else if (style[nv] == DVEC) buf[m++] = atom->dvector[index[nv]][i]; + else if (style[nv] == IARRAY) { + ncol = cols[nv]; + for (k = 0; k < ncol; k++) + buf[m++] = ubuf(atom->iarray[index[nv]][i][k]).d; + } else if (style[nv] == DARRAY) { + ncol = cols[nv]; + for (k = 0; k < ncol; k++) + buf[m++] = atom->darray[index[nv]][i][k]; + } } - return nvalue; + + return m; } /* ---------------------------------------------------------------------- @@ -558,19 +700,32 @@ int FixPropertyAtom::pack_exchange(int i, double *buf) int FixPropertyAtom::unpack_exchange(int nlocal, double *buf) { - for (int m = 0; m < nvalue; m++) { - if (style[m] == MOLECULE) - atom->molecule[nlocal] = (tagint) ubuf(buf[m]).i; - else if (style[m] == CHARGE) - atom->q[nlocal] = buf[m]; - else if (style[m] == RMASS) - atom->rmass[nlocal] = buf[m]; - else if (style[m] == INTEGER) - atom->ivector[index[m]][nlocal] = (int) ubuf(buf[m]).i; - else if (style[m] == DOUBLE) - atom->dvector[index[m]][nlocal] = buf[m]; + int k,ncol; + + int m = 0; + for (int nv = 0; nv < nvalue; nv++) { + if (style[nv] == MOLECULE) + atom->molecule[nlocal] = (tagint) ubuf(buf[m++]).i; + else if (style[nv] == CHARGE) + atom->q[nlocal] = buf[m++]; + else if (style[nv] == RMASS) + atom->rmass[nlocal] = buf[m++]; + else if (style[nv] == IVEC) + atom->ivector[index[nv]][nlocal] = (int) ubuf(buf[m++]).i; + else if (style[nv] == DVEC) + atom->dvector[index[nv]][nlocal] = buf[m++]; + else if (style[nv] == IARRAY) { + ncol = cols[nv]; + for (k = 0; k < ncol; k++) + atom->iarray[index[nv]][nlocal][k] = (int) ubuf(buf[m++]).i; + } else if (style[nv] == DARRAY) { + ncol = cols[nv]; + for (k = 0; k < ncol; k++) + atom->darray[index[nv]][nlocal][k] = buf[m++]; + } } - return nvalue; + + return m; } /* ---------------------------------------------------------------------- @@ -579,19 +734,31 @@ int FixPropertyAtom::unpack_exchange(int nlocal, double *buf) int FixPropertyAtom::pack_restart(int i, double *buf) { + int k,ncol; + // pack buf[0] this way because other fixes unpack it - buf[0] = nvalue+1; + + buf[0] = values_peratom+1; int m = 1; - for (int j = 0; j < nvalue; j++) { - if (style[j] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d; - else if (style[j] == CHARGE) buf[m++] = atom->q[i]; - else if (style[j] == RMASS) buf[m++] = atom->rmass[i]; - else if (style[j] == INTEGER) buf[m++] = ubuf(atom->ivector[index[j]][i]).d; - else if (style[j] == DOUBLE) buf[m++] = atom->dvector[index[j]][i]; + for (int nv = 0; nv < nvalue; nv++) { + if (style[nv] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d; + else if (style[nv] == CHARGE) buf[m++] = atom->q[i]; + else if (style[nv] == RMASS) buf[m++] = atom->rmass[i]; + else if (style[nv] == IVEC) buf[m++] = ubuf(atom->ivector[index[nv]][i]).d; + else if (style[nv] == DVEC) buf[m++] = atom->dvector[index[nv]][i]; + else if (style[nv] == IARRAY) { + ncol = cols[nv]; + for (k = 0; k < ncol; k++) + buf[m++] = ubuf(atom->iarray[index[nv]][i][k]).d; + } else if (style[nv] == DARRAY) { + ncol = cols[nv]; + for (k = 0; k < ncol; k++) + buf[m++] = atom->darray[index[nv]][i][k]; + } } - return nvalue+1; + return values_peratom+1; } /* ---------------------------------------------------------------------- @@ -600,6 +767,7 @@ int FixPropertyAtom::pack_restart(int i, double *buf) void FixPropertyAtom::unpack_restart(int nlocal, int nth) { + int k,ncol; double **extra = atom->extra; // skip to Nth set of extra values @@ -609,17 +777,26 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth) for (int i = 0; i < nth; i++) m += static_cast (extra[nlocal][m]); m++; - for (int i = 0; i < nvalue; i++) { - if (style[i] == MOLECULE) + for (int nv = 0; nv < nvalue; nv++) { + if (style[nv] == MOLECULE) atom->molecule[nlocal] = (tagint) ubuf(extra[nlocal][m++]).i; - else if (style[i] == CHARGE) + else if (style[nv] == CHARGE) atom->q[nlocal] = extra[nlocal][m++]; - else if (style[i] == RMASS) + else if (style[nv] == RMASS) atom->rmass[nlocal] = extra[nlocal][m++]; - else if (style[i] == INTEGER) - atom->ivector[index[i]][nlocal] = (int) ubuf(extra[nlocal][m++]).i; - else if (style[i] == DOUBLE) - atom->dvector[index[i]][nlocal] = extra[nlocal][m++]; + else if (style[nv] == IVEC) + atom->ivector[index[nv]][nlocal] = (int) ubuf(extra[nlocal][m++]).i; + else if (style[nv] == DVEC) + atom->dvector[index[nv]][nlocal] = extra[nlocal][m++]; + else if (style[nv] == IARRAY) { + ncol = cols[nv]; + for (k = 0; k < ncol; k++) + atom->iarray[index[nv]][nlocal][k] = (int) ubuf(extra[nlocal][m++]).i; + } else if (style[nv] == DARRAY) { + ncol = cols[nv]; + for (k = 0; k < ncol; k++) + atom->darray[index[nv]][nlocal][k] = extra[nlocal][m++]; + } } } @@ -629,7 +806,7 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth) int FixPropertyAtom::maxsize_restart() { - return nvalue+1; + return values_peratom+1; } /* ---------------------------------------------------------------------- @@ -638,5 +815,5 @@ int FixPropertyAtom::maxsize_restart() int FixPropertyAtom::size_restart(int /*nlocal*/) { - return nvalue+1; + return values_peratom+1; } diff --git a/src/fix_property_atom.h b/src/fix_property_atom.h index 9e0236f61e..3e491ea861 100644 --- a/src/fix_property_atom.h +++ b/src/fix_property_atom.h @@ -52,10 +52,13 @@ class FixPropertyAtom : public Fix { protected: int nvalue,border; - int molecule_flag,q_flag,rmass_flag; - int *style,*index; - char *astyle; + int molecule_flag,q_flag,rmass_flag; // flags for specific fields + int *style; // style of each value, see enum + int *index; // indices into atom custom data structs + int *cols; // columns per value, for arrays + char *astyle; // atom style at instantiation + int values_peratom; // # of values per atom, including multiple for arrays int nmax_old; // length of peratom arrays the last time they grew }; diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp index e1e2aab663..cdda399fff 100644 --- a/src/fix_store_state.cpp +++ b/src/fix_store_state.cpp @@ -20,17 +20,18 @@ #include "group.h" #include "modify.h" #include "compute.h" +#include "force.h" #include "fix.h" #include "input.h" #include "variable.h" +#include "utils.h" #include "memory.h" #include "error.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; -enum{KEYWORD,COMPUTE,FIX,VARIABLE,DNAME,INAME}; +enum{KEYWORD,COMPUTE,FIX,VARIABLE,IVEC,DVEC,IARRAY,DARRAY}; #define INVOKED_PERATOM 8 @@ -224,15 +225,11 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) : pack_choice[nvalues++] = &FixStoreState::pack_tqz; } else if (strncmp(arg[iarg],"c_",2) == 0 || - strncmp(arg[iarg],"d_",2) == 0 || strncmp(arg[iarg],"f_",2) == 0 || - strncmp(arg[iarg],"i_",2) == 0 || strncmp(arg[iarg],"v_",2) == 0) { cfv_any = 1; if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE; - else if (arg[iarg][0] == 'd') which[nvalues] = DNAME; else if (arg[iarg][0] == 'f') which[nvalues] = FIX; - else if (arg[iarg][0] == 'i') which[nvalues] = INAME; else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE; int n = strlen(arg[iarg]); @@ -241,11 +238,50 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) : char *ptr = strchr(suffix,'['); if (ptr) { + if (which[nvalues] == VARIABLE) + error->all(FLERR,"Illegal fix store/state command"); if (suffix[strlen(suffix)-1] != ']') error->all(FLERR,"Illegal fix store/state command"); - argindex[nvalues] = atoi(ptr+1); + suffix[strlen(suffix)-1] = '\0'; + argindex[nvalues] = utils::inumeric(FLERR,ptr+1,true,lmp); *ptr = '\0'; } else argindex[nvalues] = 0; + + n = strlen(suffix) + 1; + ids[nvalues] = new char[n]; + strcpy(ids[nvalues],suffix); + nvalues++; + delete [] suffix; + + } else if (strncmp(arg[iarg],"i_",2) == 0 || + strncmp(arg[iarg],"d_",2) == 0 || + strncmp(arg[iarg],"i2_",3) == 0 || + strncmp(arg[iarg],"d2_",3) == 0) { + if (strncmp(arg[iarg],"i_",2) == 0) which[nvalues] = IVEC; + else if (strncmp(arg[iarg],"d_",2) == 0) which[nvalues] = DVEC; + else if (strncmp(arg[iarg],"i2_",3) == 0) which[nvalues] = IARRAY; + else if (strncmp(arg[iarg],"d2_",3) == 0) which[nvalues] = DARRAY; + + int n = strlen(arg[iarg]); + char *suffix = new char[n]; + if (which[nvalues] == IVEC || which[nvalues] == DVEC) + strcpy(suffix,&arg[iarg][2]); + else strcpy(suffix,&arg[iarg][3]); + + char *ptr = strchr(suffix,'['); + if (ptr) { + if (which[nvalues] == IVEC || which[nvalues] == DVEC) + error->all(FLERR,"Illegal fix store/state command"); + if (suffix[strlen(suffix)-1] != ']') + error->all(FLERR,"Illegal fix store/state command"); + suffix[strlen(suffix)-1] = '\0'; + argindex[nvalues] = utils::inumeric(FLERR,ptr+1,true,lmp); + *ptr = '\0'; + } else { + if (which[nvalues] == IARRAY || which[nvalues] == DARRAY) + error->all(FLERR,"Illegal fix store/state command"); + argindex[nvalues] = 0; + } n = strlen(suffix) + 1; ids[nvalues] = new char[n]; @@ -274,68 +310,79 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) : // error check - for (int i = 0; i < nvalues; i++) { - if (which[i] == COMPUTE) { - int icompute = modify->find_compute(ids[i]); + for (int m = 0; m < nvalues; m++) { + if (which[m] == COMPUTE) { + int icompute = modify->find_compute(ids[m]); if (icompute < 0) error->all(FLERR,"Compute ID for fix store/state does not exist"); if (modify->compute[icompute]->peratom_flag == 0) error->all(FLERR,"Fix store/state compute " "does not calculate per-atom values"); - if (argindex[i] == 0 && + if (argindex[m] == 0 && modify->compute[icompute]->size_peratom_cols != 0) error->all(FLERR,"Fix store/state compute does not " "calculate a per-atom vector"); - if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0) + if (argindex[m] && modify->compute[icompute]->size_peratom_cols == 0) error->all(FLERR, "Fix store/state compute does not " "calculate a per-atom array"); - if (argindex[i] && - argindex[i] > modify->compute[icompute]->size_peratom_cols) + if (argindex[m] && + argindex[m] > modify->compute[icompute]->size_peratom_cols) error->all(FLERR, "Fix store/state compute array is accessed out-of-range"); - - } else if (which[i] == INAME) { - int icustom,iflag; - icustom = atom->find_custom(ids[i],iflag); - if ((icustom < 0) || (iflag != 0)) - error->all(FLERR, - "Custom integer vector for fix store/state does not exist"); - - } else if (which[i] == DNAME) { - int icustom,iflag; - icustom = atom->find_custom(ids[i],iflag); - if ((icustom < 0) || (iflag != 1)) - error->all(FLERR, - "Custom floating point vector for fix store/state does not exist"); - - } else if (which[i] == FIX) { - int ifix = modify->find_fix(ids[i]); + + } else if (which[m] == FIX) { + int ifix = modify->find_fix(ids[m]); if (ifix < 0) error->all(FLERR, "Fix ID for fix store/state does not exist"); if (modify->fix[ifix]->peratom_flag == 0) error->all(FLERR, "Fix store/state fix does not calculate per-atom values"); - if (argindex[i] == 0 && modify->fix[ifix]->size_peratom_cols != 0) + if (argindex[m] == 0 && modify->fix[ifix]->size_peratom_cols != 0) error->all(FLERR, "Fix store/state fix does not calculate a per-atom vector"); - if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0) + if (argindex[m] && modify->fix[ifix]->size_peratom_cols == 0) error->all(FLERR, "Fix store/state fix does not calculate a per-atom array"); - if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols) + if (argindex[m] && argindex[m] > modify->fix[ifix]->size_peratom_cols) error->all(FLERR, "Fix store/state fix array is accessed out-of-range"); if (nevery % modify->fix[ifix]->peratom_freq) error->all(FLERR, "Fix for fix store/state not computed at compatible time"); - } else if (which[i] == VARIABLE) { - int ivariable = input->variable->find(ids[i]); + } else if (which[m] == VARIABLE) { + int ivariable = input->variable->find(ids[m]); if (ivariable < 0) error->all(FLERR,"Variable name for fix store/state does not exist"); if (input->variable->atomstyle(ivariable) == 0) error->all(FLERR,"Fix store/state variable is not atom-style variable"); + + } else if (which[m] == IVEC) { + int icustom,flag,cols; + icustom = atom->find_custom(ids[m],flag,cols); + if ((icustom < 0) || flag || cols) + error->all(FLERR, + "Custom integer vector for fix store/state does not exist"); + } else if (which[m] == DVEC) { + int icustom,flag,cols; + icustom = atom->find_custom(ids[m],flag,cols); + if ((icustom < 0) || !flag || cols) + error->all(FLERR, + "Custom floating point vector for fix store/state does not exist"); + } else if (which[m] == IARRAY) { + int icustom,flag,cols; + icustom = atom->find_custom(ids[m],flag,cols); + if ((icustom < 0) || flag || !cols) + error->all(FLERR, + "Custom integer array for fix store/state does not exist"); + } else if (which[m] == DARRAY) { + int icustom,flag,cols; + icustom = atom->find_custom(ids[m],flag,cols); + if ((icustom < 0) || !flag || !cols) + error->all(FLERR, + "Custom floating point array for fix store/state does not exist"); } } @@ -413,22 +460,6 @@ void FixStoreState::init() error->all(FLERR,"Compute ID for fix store/state does not exist"); value2index[m] = icompute; - } else if (which[m] == INAME) { - int icustom,iflag; - icustom = atom->find_custom(ids[m],iflag); - if ((icustom < 0) || (iflag != 0)) - error->all(FLERR, - "Custom integer vector for fix store/state does not exist"); - value2index[m] = icustom; - - } else if (which[m] == DNAME) { - int icustom,iflag; - icustom = atom->find_custom(ids[m],iflag); - if ((icustom < 0) || (iflag != 1)) - error->all(FLERR, - "Custom floating point vector for fix store/state does not exist"); - value2index[m] = icustom; - } else if (which[m] == FIX) { int ifix = modify->find_fix(ids[m]); if (ifix < 0) @@ -440,6 +471,35 @@ void FixStoreState::init() if (ivariable < 0) error->all(FLERR,"Variable name for fix store/state does not exist"); value2index[m] = ivariable; + + } else if (which[m] == IVEC) { + int icustom,flag,cols; + icustom = atom->find_custom(ids[m],flag,cols); + if (icustom < 0 || flag || cols) + error->all(FLERR, + "Custom integer vector for fix store/state does not exist"); + value2index[m] = icustom; + } else if (which[m] == DVEC) { + int icustom,flag,cols; + icustom = atom->find_custom(ids[m],flag,cols); + if (icustom < 0 || !flag || cols) + error->all(FLERR, + "Custom floating point vector for fix store/state does not exist"); + value2index[m] = icustom; + } else if (which[m] == IARRAY) { + int icustom,flag,cols; + icustom = atom->find_custom(ids[m],flag,cols); + if (icustom < 0 || flag || !cols) + error->all(FLERR, + "Custom integer array for fix store/state does not exist"); + value2index[m] = icustom; + } else if (which[m] == DARRAY) { + int icustom,flag,cols; + icustom = atom->find_custom(ids[m],flag,cols); + if (icustom < 0 || !flag || !cols) + error->all(FLERR, + "Custom floating point array for fix store/state does not exist"); + value2index[m] = icustom; } } } @@ -525,22 +585,33 @@ void FixStoreState::end_of_step() if (mask[i] & groupbit) values[i][m] = fix_array[i][jm1]; } - // access custom atom property fields - - } else if (which[m] == INAME) { - int *ivector = atom->ivector[n]; - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) values[i][m] = ivector[i]; - - } else if (which[m] == DNAME) { - double *dvector = atom->dvector[n]; - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) values[i][m] = dvector[i]; - // evaluate atom-style variable } else if (which[m] == VARIABLE) { input->variable->compute_atom(n,igroup,&values[0][m],nvalues,0); + + // access custom atom property fields + + } else if (which[m] == IVEC) { + int *ivector = atom->ivector[n]; + for (i = 0; i < nlocal; i++) + if (mask[i] & groupbit) values[i][m] = ivector[i]; + } else if (which[m] == DVEC) { + double *dvector = atom->dvector[n]; + for (i = 0; i < nlocal; i++) + if (mask[i] & groupbit) values[i][m] = dvector[i]; + } else if (which[m] == IARRAY) { + int **iarray = atom->iarray[n]; + int jm1 = j - 1; + for (i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + values[i][m] = iarray[i][jm1]; + } else if (which[m] == DARRAY) { + double **darray = atom->darray[n]; + int jm1 = j - 1; + for (i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + values[i][m] = darray[i][jm1]; } } } diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp index 919d1f3f61..f42e8df031 100644 --- a/src/imbalance_store.cpp +++ b/src/imbalance_store.cpp @@ -47,18 +47,17 @@ int ImbalanceStore::options(int narg, char **arg) void ImbalanceStore::compute(double *weight) { - int dflag = 0; - int idx = atom->find_custom(name,dflag); + int flag,cols; + int index = atom->find_custom(name,flag,cols); // property does not exist - if (idx < 0 || dflag != 1) return; + if (index < 0 || flag != 1 || cols) + error->all(FLERR,"Balance weight store vector does not exist"); - double *prop = atom->dvector[idx]; + double *prop = atom->dvector[index]; const int nlocal = atom->nlocal; - - for (int i = 0; i < nlocal; ++i) - prop[i] = weight[i]; + for (int i = 0; i < nlocal; ++i) prop[i] = weight[i]; } /* -------------------------------------------------------------------- */ diff --git a/src/input.cpp b/src/input.cpp index dd640f18b0..1069cbf944 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -600,8 +600,9 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag) } /* ---------------------------------------------------------------------- - expand arg to earg, for arguments with syntax c_ID[*] or f_ID[*] + expand arg to earg, for args with syntax c_ID[*], f_ID[*], i2_ID[*], d2_ID[*] fields to consider in input arg range from iarg to narg + mode = 0 for args = vectors, mode = 1 for args = arrays return new expanded # of values, and copy them w/out "*" into earg if any expansion occurs, earg is new allocation, must be freed by caller if no expansion occurs, earg just points to arg, caller need not free @@ -609,7 +610,7 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag) int Input::expand_args(int narg, char **arg, int mode, char **&earg) { - int n,iarg,index,nlo,nhi,nmax,expandflag,icompute,ifix; + int n,iarg,index,nlo,nhi,nmax,expandflag; char *ptr1,*ptr2,*str; ptr1 = NULL; @@ -633,7 +634,9 @@ int Input::expand_args(int narg, char **arg, int mode, char **&earg) expandflag = 0; if (strncmp(arg[iarg],"c_",2) == 0 || - strncmp(arg[iarg],"f_",2) == 0) { + strncmp(arg[iarg],"f_",2) == 0 || + strncmp(arg[iarg],"i2_",3) == 0 || + strncmp(arg[iarg],"d2_",3) == 0) { ptr1 = strchr(&arg[iarg][2],'['); if (ptr1) { @@ -641,9 +644,10 @@ int Input::expand_args(int narg, char **arg, int mode, char **&earg) if (ptr2) { *ptr2 = '\0'; if (strchr(ptr1,'*')) { + if (arg[iarg][0] == 'c') { *ptr1 = '\0'; - icompute = modify->find_compute(&arg[iarg][2]); + int icompute = modify->find_compute(&arg[iarg][2]); *ptr1 = '['; // check for global vector/array, peratom array, local array @@ -665,9 +669,10 @@ int Input::expand_args(int narg, char **arg, int mode, char **&earg) expandflag = 1; } } + } else if (arg[iarg][0] == 'f') { *ptr1 = '\0'; - ifix = modify->find_fix(&arg[iarg][2]); + int ifix = modify->find_fix(&arg[iarg][2]); *ptr1 = '['; // check for global vector/array, peratom array, local array @@ -689,10 +694,40 @@ int Input::expand_args(int narg, char **arg, int mode, char **&earg) expandflag = 1; } } - } - } - *ptr2 = ']'; - } + + } else if (arg[iarg][0] == 'i') { + *ptr1 = '\0'; + int flag,cols; + int icustom = atom->find_custom(&arg[iarg][3],flag,cols); + *ptr1 = '['; + + // check for custom per-atom integer array + + if (icustom >= 0) { + if (mode == 1 && !flag && cols) { + nmax = cols; + expandflag = 1; + } + } + + } else if (arg[iarg][0] == 'd') { + *ptr1 = '\0'; + int flag,cols; + int icustom = atom->find_custom(&arg[iarg][3],flag,cols); + *ptr1 = '['; + + // check for custom per-atom floating point array + + if (icustom >= 0) { + if (mode == 1 && flag && cols) { + nmax = cols; + expandflag = 1; + } + } + } + } + *ptr2 = ']'; + } } } diff --git a/src/set.cpp b/src/set.cpp index 01176f68c0..d7a8337f81 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -45,12 +45,12 @@ using namespace MathConst; enum{ATOM_SELECT,MOL_SELECT,TYPE_SELECT,GROUP_SELECT,REGION_SELECT}; enum{TYPE,TYPE_FRACTION,TYPE_RATIO,TYPE_SUBSET, - MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,LENGTH,TRI, + MOLECULE,X,Y,Z,VX,VY,VZ,CHARGE,MASS,SHAPE,LENGTH,TRI, DIPOLE,DIPOLE_RANDOM,SPIN,SPIN_RANDOM,QUAT,QUAT_RANDOM, THETA,THETA_RANDOM,ANGMOM,OMEGA, DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER, SPH_E,SPH_CV,SPH_RHO,EDPD_TEMP,EDPD_CV,CC,SMD_MASS_DENSITY, - SMD_CONTACT_RADIUS,DPDTHETA,INAME,DNAME,VX,VY,VZ}; + SMD_CONTACT_RADIUS,DPDTHETA,IVEC,DVEC,IARRAY,DARRAY}; #define BIG INT_MAX @@ -573,28 +573,63 @@ void Set::command(int narg, char **arg) set(DPDTHETA); iarg += 2; - } else if (strstr(arg[iarg],"i_") == arg[iarg]) { - if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); - if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); - else ivalue = force->inumeric(FLERR,arg[iarg+1]); - int flag; - index_custom = atom->find_custom(&arg[iarg][2],flag); - if (index_custom < 0 || flag != 0) - error->all(FLERR,"Set command integer vector does not exist"); - set(INAME); - iarg += 2; - - } else if (strstr(arg[iarg],"d_") == arg[iarg]) { + // custom per-atom vector + + } else if (strstr(arg[iarg],"i_") == arg[iarg] || + strstr(arg[iarg],"d_") == arg[iarg]) { if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); + int which = 0; + if (arg[iarg][0] == 'd') which = 1; if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else if (!which) ivalue = force->inumeric(FLERR,arg[iarg+1]); else dvalue = force->numeric(FLERR,arg[iarg+1]); - int flag; - index_custom = atom->find_custom(&arg[iarg][2],flag); - if (index_custom < 0 || flag != 1) - error->all(FLERR,"Set command floating point vector does not exist"); - set(DNAME); + + int flag,cols; + index_custom = atom->find_custom(&arg[iarg][2],flag,cols); + if ((!which && (index_custom < 0 || flag || cols)) || + (which && (index_custom < 0 || !flag || cols))) + error->all(FLERR,"Set command per-atom custom vector does not exist"); + if (!which) set(IVEC); + else set(DVEC); iarg += 2; + // custom per-atom array, must include bracketed index + + } else if (strstr(arg[iarg],"i2_") == arg[iarg] || + strstr(arg[iarg],"d2_") == arg[iarg]) { + if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); + int which = 0; + if (arg[iarg][0] == 'd') which = 1; + if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else if (!which) ivalue = force->inumeric(FLERR,arg[iarg+1]); + else dvalue = force->numeric(FLERR,arg[iarg+1]); + + int n = strlen(arg[iarg]); + char *suffix = new char[n]; + strcpy(suffix,&arg[iarg][3]); + + char *ptr = strchr(suffix,'['); + if (ptr) { + if (suffix[strlen(suffix)-1] != ']') + error->all(FLERR,"Invalid attribute in set command"); + icol_custom = atoi(ptr+1); + *ptr = '\0'; + } else error->all(FLERR,"Set command per-atom custom array is not indexed"); + + int flag,cols; + index_custom = atom->find_custom(suffix,flag,cols); + delete [] suffix; + + if ((!which && (index_custom < 0 || flag || !cols)) || + (which && (index_custom < 0 || !flag || !cols))) + error->all(FLERR,"Set command per-atom custom array does not exist"); + if (icol_custom <= 0 || icol_custom > cols) + error->all(FLERR,"Set command per-atom custom array is accessed out-of-range"); + + if (!which) set(IARRAY); + else set(DARRAY); + iarg += 2; + } else error->all(FLERR,"Illegal set command"); // statistics @@ -970,20 +1005,29 @@ void Set::set(int keyword) (((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS); } - // set value for custom integer or double vector + // set value for custom vector or array - else if (keyword == INAME) { + else if (keyword == IVEC) { atom->ivector[index_custom][i] = ivalue; } - else if (keyword == DNAME) { + else if (keyword == DVEC) { atom->dvector[index_custom][i] = dvalue; } + else if (keyword == IARRAY) { + atom->iarray[index_custom][i][icol_custom-1] = ivalue; + } + + else if (keyword == DARRAY) { + atom->darray[index_custom][i][icol_custom-1] = dvalue; + } + count++; } // update bonus data numbers + if (keyword == SHAPE) { bigint nlocal_bonus = avec_ellipsoid->nlocal_bonus; MPI_Allreduce(&nlocal_bonus,&atom->nellipsoids,1, diff --git a/src/set.h b/src/set.h index 6788849677..bbbe08bc47 100644 --- a/src/set.h +++ b/src/set.h @@ -32,7 +32,7 @@ class Set : protected Pointers { private: char *id; int *select; - int style,ivalue,newtype,count,index_custom; + int style,ivalue,newtype,count,index_custom,icol_custom; int ximage,yimage,zimage,ximageflag,yimageflag,zimageflag; int cc_index; bigint nsubset;