diff --git a/doc/src/Eqs/fix_mvv_dpd.jpg b/doc/src/Eqs/fix_mvv_dpd.jpg new file mode 100644 index 0000000000..f62ae28bc4 Binary files /dev/null and b/doc/src/Eqs/fix_mvv_dpd.jpg differ diff --git a/doc/src/Eqs/fix_mvv_dpd.tex b/doc/src/Eqs/fix_mvv_dpd.tex new file mode 100644 index 0000000000..4652d54b77 --- /dev/null +++ b/doc/src/Eqs/fix_mvv_dpd.tex @@ -0,0 +1,21 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + v(t+\frac{\Delta t}{2}) = v(t) + \frac{\Delta t}{2}\cdot a(t), +$$ + +$$ + r(t+\Delta t) = r(t) + \Delta t\cdot v(t+\frac{\Delta t}{2}), +$$ + +$$ + a(t+\Delta t) = \frac{1}{m}\cdot F\left[ r(t+\Delta t), v(t) +\lambda \cdot \Delta t\cdot a(t)\right], +$$ + +$$ + v(t+\Delta t) = v(t+\frac{\Delta t}{2}) + \frac{\Delta t}{2}\cdot a(t++\Delta t), +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_edpd_force.jpg b/doc/src/Eqs/pair_edpd_force.jpg new file mode 100644 index 0000000000..fabb6f772e Binary files /dev/null and b/doc/src/Eqs/pair_edpd_force.jpg differ diff --git a/doc/src/Eqs/pair_edpd_force.tex b/doc/src/Eqs/pair_edpd_force.tex new file mode 100644 index 0000000000..f6a0ca0d3c --- /dev/null +++ b/doc/src/Eqs/pair_edpd_force.tex @@ -0,0 +1,33 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + \mathbf{F}_{ij}^{C} = \alpha_{ij}{\omega_{C}}(r_{ij})\mathbf{e}_{ij}, +$$ + +$$ + \mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij}, +$$ + +$$ + \mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij}, +$$ + +$$ + \omega_{C}(r) = 1 - r/r_c, +$$ + +$$ + \alpha_{ij} = A\cdot k_B(T_i + T_j)/2, +$$ + +$$ + \omega_{D}(r) = \omega^2_{R}(r) = (1-r/r_c)^s, +$$ + +$$ + \sigma_{ij}^2 = 4\gamma k_B T_i T_j/(T_i + T_j), +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_edpd_gov.jpg b/doc/src/Eqs/pair_edpd_gov.jpg new file mode 100644 index 0000000000..10b303a218 Binary files /dev/null and b/doc/src/Eqs/pair_edpd_gov.jpg differ diff --git a/doc/src/Eqs/pair_edpd_gov.tex b/doc/src/Eqs/pair_edpd_gov.tex new file mode 100644 index 0000000000..782cdec99e --- /dev/null +++ b/doc/src/Eqs/pair_edpd_gov.tex @@ -0,0 +1,15 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + \frac{\mathrm{d}^2 \mathbf{r}_i}{\mathrm{d} t^2}= + \frac{\mathrm{d} \mathbf{v}_i}{\mathrm{d} t} + =\mathbf{F}_{i}=\sum_{i\neq j}(\mathbf{F}_{ij}^{C}+\mathbf{F}_{ij}^{D}+\mathbf{F}_{ij}^{R}), +$$ + +$$ + C_v\frac{\mathrm{d} T_i}{\mathrm{d} t}= q_{i} = \sum_{i\neq j}(q_{ij}^{C}+q_{ij}^{V}+q_{ij}^{R}), +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_edpd_heat.jpg b/doc/src/Eqs/pair_edpd_heat.jpg new file mode 100644 index 0000000000..b9256a1d13 Binary files /dev/null and b/doc/src/Eqs/pair_edpd_heat.jpg differ diff --git a/doc/src/Eqs/pair_edpd_heat.tex b/doc/src/Eqs/pair_edpd_heat.tex new file mode 100644 index 0000000000..241a1bad64 --- /dev/null +++ b/doc/src/Eqs/pair_edpd_heat.tex @@ -0,0 +1,29 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + q_i^C = \sum_{j \ne i} k_{ij} \omega_{CT}(r_{ij}) \left( \frac{1}{T_i} - \frac{1}{T_j} \right), +$$ + +$$ + q_i^V = \frac{1}{2 C_v}\sum_{j \ne i}{ \left\{ \omega_D(r_{ij})\left[\gamma_{ij} \left( \mathbf{e}_{ij} \cdot \mathbf{v}_{ij} \right)^2 - \frac{\left( \sigma _{ij} \right)^2}{m}\right] - \sigma _{ij} \omega_R(r_{ij})\left( \mathbf{e}_{ij} \cdot \mathbf{v}_{ij} \right){\xi_{ij}} \right\} }, +$$ + +$$ + q_i^R = \sum_{j \ne i} \beta _{ij} \omega_{RT}(r_{ij}) d {t^{ - 1/2}} \xi_{ij}^e, +$$ + +$$ + \omega_{CT}(r)=\omega_{RT}^2(r)=\left(1-r/r_{ct}\right)^{s_T}, +$$ + +$$ + k_{ij}=C_v^2\kappa(T_i + T_j)^2/4k_B, +$$ + +$$ + \beta_{ij}^2=2k_Bk_{ij}, +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_edpd_kappa.jpg b/doc/src/Eqs/pair_edpd_kappa.jpg new file mode 100644 index 0000000000..158974d374 Binary files /dev/null and b/doc/src/Eqs/pair_edpd_kappa.jpg differ diff --git a/doc/src/Eqs/pair_edpd_kappa.tex b/doc/src/Eqs/pair_edpd_kappa.tex new file mode 100644 index 0000000000..ac5ca9f740 --- /dev/null +++ b/doc/src/Eqs/pair_edpd_kappa.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + \kappa = \frac{315k_B\upsilon }{2\pi \rho C_v r_{ct}^5}\frac{1}{Pr}, +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_mdpd_force.jpg b/doc/src/Eqs/pair_mdpd_force.jpg new file mode 100644 index 0000000000..9b0e573b79 Binary files /dev/null and b/doc/src/Eqs/pair_mdpd_force.jpg differ diff --git a/doc/src/Eqs/pair_mdpd_force.tex b/doc/src/Eqs/pair_mdpd_force.tex new file mode 100644 index 0000000000..b5c8d9be4a --- /dev/null +++ b/doc/src/Eqs/pair_mdpd_force.tex @@ -0,0 +1,17 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + \mathbf{F}_{ij}^C = Aw_c(r_{ij})\mathbf{e}_{ij} + B(\rho_i+\rho_j)w_d(r_{ij})\mathbf{e}_{ij}, +$$ + +$$ + \mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij}, +$$ + +$$ + \mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij}, +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_tdpd_flux.jpg b/doc/src/Eqs/pair_tdpd_flux.jpg new file mode 100644 index 0000000000..9da788ae9b Binary files /dev/null and b/doc/src/Eqs/pair_tdpd_flux.jpg differ diff --git a/doc/src/Eqs/pair_tdpd_flux.tex b/doc/src/Eqs/pair_tdpd_flux.tex new file mode 100644 index 0000000000..f753f16acf --- /dev/null +++ b/doc/src/Eqs/pair_tdpd_flux.tex @@ -0,0 +1,21 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + Q_{ij}^D = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right), +$$ + +$$ + Q_{ij}^R = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij}, +$$ + +$$ + w_{DC}(r_{ij})=w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power\_{cc}}, +$$ + +$$ + \epsilon_{ij}^2 = m_s^2\kappa_{ij}\rho, +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_tdpd_force.jpg b/doc/src/Eqs/pair_tdpd_force.jpg new file mode 100644 index 0000000000..f6feb35397 Binary files /dev/null and b/doc/src/Eqs/pair_tdpd_force.jpg differ diff --git a/doc/src/Eqs/pair_tdpd_force.tex b/doc/src/Eqs/pair_tdpd_force.tex new file mode 100644 index 0000000000..49edff9700 --- /dev/null +++ b/doc/src/Eqs/pair_tdpd_force.tex @@ -0,0 +1,29 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + \mathbf{F}_{ij}^{C} = A{\omega_{C}}(r_{ij})\mathbf{e}_{ij}, +$$ + +$$ + \mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij}, +$$ + +$$ + \mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij}, +$$ + +$$ + \omega_{C}(r) = 1 - r/r_c, +$$ + +$$ + \omega_{D}(r) = \omega^2_{R}(r) = (1-r/r_c)^{\rm power\_f}, +$$ + +$$ + \sigma^2 = 2\gamma k_B T, +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_tdpd_gov.jpg b/doc/src/Eqs/pair_tdpd_gov.jpg new file mode 100644 index 0000000000..0ed793a132 Binary files /dev/null and b/doc/src/Eqs/pair_tdpd_gov.jpg differ diff --git a/doc/src/Eqs/pair_tdpd_gov.tex b/doc/src/Eqs/pair_tdpd_gov.tex new file mode 100644 index 0000000000..e4b5f5790a --- /dev/null +++ b/doc/src/Eqs/pair_tdpd_gov.tex @@ -0,0 +1,13 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + \frac{\mathrm{d}^2 \mathbf{r}_i}{\mathrm{d} t^2} = \frac{\mathrm{d} \mathbf{v}_i}{\mathrm{d} t}=\mathbf{F}_{i}=\sum_{i\neq j}(\mathbf{F}_{ij}^{C}+\mathbf{F}_{ij}^{D}+\mathbf{F}_{ij}^{R}), +$$ + +$$ + \frac{\mathrm{d} C_{i}}{\mathrm{d} t}= Q_{i} = \sum_{i\neq j}(Q_{ij}^{D}+Q_{ij}^{R}) + Q_{i}^{S}, +$$ + +\end{document} diff --git a/doc/src/JPG/examples_edpd.jpg b/doc/src/JPG/examples_edpd.jpg new file mode 100644 index 0000000000..4d0cde6370 Binary files /dev/null and b/doc/src/JPG/examples_edpd.jpg differ diff --git a/doc/src/JPG/examples_mdpd.gif b/doc/src/JPG/examples_mdpd.gif new file mode 100644 index 0000000000..29ace1a0b2 Binary files /dev/null and b/doc/src/JPG/examples_mdpd.gif differ diff --git a/doc/src/JPG/examples_mdpd_first.jpg b/doc/src/JPG/examples_mdpd_first.jpg new file mode 100644 index 0000000000..958912e662 Binary files /dev/null and b/doc/src/JPG/examples_mdpd_first.jpg differ diff --git a/doc/src/JPG/examples_mdpd_last.jpg b/doc/src/JPG/examples_mdpd_last.jpg new file mode 100644 index 0000000000..1bf8b9ac82 Binary files /dev/null and b/doc/src/JPG/examples_mdpd_last.jpg differ diff --git a/doc/src/JPG/examples_tdpd.jpg b/doc/src/JPG/examples_tdpd.jpg new file mode 100644 index 0000000000..c00e83e003 Binary files /dev/null and b/doc/src/JPG/examples_tdpd.jpg differ diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 571c6c4920..fda727ec05 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -685,6 +685,7 @@ package"_Section_start.html#start_3. "drude"_fix_drude.html, "drude/transform/direct"_fix_drude_transform.html, "drude/transform/reverse"_fix_drude_transform.html, +"edpd/source"_fix_dpd_source.html, "eos/cv"_fix_eos_cv.html, "eos/table"_fix_eos_table.html, "eos/table/rx"_fix_eos_table_rx.html, @@ -704,6 +705,9 @@ package"_Section_start.html#start_3. "meso"_fix_meso.html, "manifoldforce"_fix_manifoldforce.html, "meso/stationary"_fix_meso_stationary.html, +"mvv/dpd"_fix_mvv_dpd.html, +"mvv/edpd"_fix_mvv_dpd.html, +"mvv/tdpd"_fix_mvv_dpd.html, "nve/dot"_fix_nve_dot.html, "nve/dotc/langevin"_fix_nve_dotc_langevin.html, "nve/manifold/rattle"_fix_nve_manifold_rattle.html, @@ -732,6 +736,7 @@ package"_Section_start.html#start_3. "smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html, "smd/setvel"_fix_smd_setvel.html, "smd/wall/surface"_fix_smd_wall_surface.html, +"tdpd/source"_fix_dpd_source.html, "temp/rescale/eff"_fix_temp_rescale_eff.html, "ti/spring"_fix_ti_spring.html, "ttm/mod"_fix_ttm.html, @@ -836,6 +841,7 @@ package"_Section_start.html#start_3. "cnp/atom"_compute_cnp_atom.html, "dpd"_compute_dpd.html, "dpd/atom"_compute_dpd_atom.html, +"edpd/temp/atom"_compute_edpd_temp_atom.html, "fep"_compute_fep.html, "force/tally"_compute_tally.html, "heat/flux/tally"_compute_tally.html, @@ -868,6 +874,7 @@ package"_Section_start.html#start_3. "smd/ulsph/stress"_compute_smd_ulsph_stress.html, "smd/vol"_compute_smd_vol.html, "stress/tally"_compute_tally.html, +"tdpd/cc/atom"_compute_tdpd_cc_atom.html, "temp/drude"_compute_temp_drude.html, "temp/eff"_compute_temp_eff.html, "temp/deform/eff"_compute_temp_deform_eff.html, @@ -1024,6 +1031,7 @@ package"_Section_start.html#start_3. "eam/cd (o)"_pair_eam.html, "edip (o)"_pair_edip.html, "edip/multi"_pair_edip.html, +"edpd"_pair_meso.html, "eff/cut"_pair_eff.html, "exp6/rx"_pair_exp6_rx.html, "gauss/cut"_pair_gauss.html, @@ -1041,6 +1049,8 @@ package"_Section_start.html#start_3. "lj/sdk (gko)"_pair_sdk.html, "lj/sdk/coul/long (go)"_pair_sdk.html, "lj/sdk/coul/msm (o)"_pair_sdk.html, +"mdpd"_pair_meso.html, +"mdpd/rhosum"_pair_meso.html, "meam/c"_pair_meam.html, "meam/spline (o)"_pair_meam_spline.html, "meam/sw/spline"_pair_meam_sw_spline.html, @@ -1074,6 +1084,7 @@ package"_Section_start.html#start_3. "sph/taitwater/morris"_pair_sph_taitwater_morris.html, "srp"_pair_srp.html, "table/rx"_pair_table_rx.html, +"tdpd"_pair_meso.html, "tersoff/table (o)"_pair_tersoff.html, "thole"_pair_thole.html, "tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index 16864bcdc4..6122dfac78 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -112,7 +112,7 @@ Package, Description, Doc page, Example, Library "REPLICA"_#REPLICA, multi-replica methods, "Section 6.6.5"_Section_howto.html#howto_5, tad, - "RIGID"_#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, - "SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, - -"SNAP"_#SNAP, quantum-fitted potential, "pair snap"_pair_snap.html, snap, - +"SNAP"_#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, - "SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, - "VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l) @@ -134,6 +134,7 @@ Package, Description, Doc page, Example, Library "USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, - "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, - "USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, - +"USER-MESO"_#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, - "USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, - "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, - "USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext @@ -1342,7 +1343,7 @@ make machine :pre [Supporting info:] src/SNAP: filenames -> commands -"pair snap"_pair_snap.html +"pair_style snap"_pair_snap.html "compute sna/atom"_compute_sna_atom.html "compute snad/atom"_compute_sna_atom.html "compute snav/atom"_compute_sna_atom.html @@ -1556,7 +1557,7 @@ make machine :pre src/USER-AWPMD: filenames -> commands src/USER-AWPMD/README -"pair awpmd/cut"_pair_awpmd.html +"pair_style awpmd/cut"_pair_awpmd.html examples/USER/awpmd :ul :line @@ -1745,12 +1746,12 @@ src/USER-DPD: filenames -> commands "fix eos/table/rx"_fix_eos_table_rx.html "fix shardlow"_fix_shardlow.html "fix rx"_fix_rx.html -"pair table/rx"_pair_table_rx.html -"pair dpd/fdt"_pair_dpd_fdt.html -"pair dpd/fdt/energy"_pair_dpd_fdt.html -"pair exp6/rx"_pair_exp6_rx.html -"pair multi/lucy"_pair_multi_lucy.html -"pair multi/lucy/rx"_pair_multi_lucy_rx.html +"pair_style table/rx"_pair_table_rx.html +"pair_style dpd/fdt"_pair_dpd_fdt.html +"pair_style dpd/fdt/energy"_pair_dpd_fdt.html +"pair_style exp6/rx"_pair_exp6_rx.html +"pair_style multi/lucy"_pair_multi_lucy.html +"pair_style multi/lucy/rx"_pair_multi_lucy_rx.html examples/USER/dpd :ul :line @@ -1785,8 +1786,8 @@ src/USER-DRUDE/README "fix drude"_fix_drude.html "fix drude/transform/*"_fix_drude_transform.html "compute temp/drude"_compute_temp_drude.html -"pair thole"_pair_thole.html -"pair lj/cut/thole/long"_pair_thole.html +"pair_style thole"_pair_thole.html +"pair_style lj/cut/thole/long"_pair_thole.html examples/USER/drude tools/drude :ul @@ -1824,8 +1825,8 @@ src/USER-EFF/README "fix npt/eff"_fix_nh_eff.html "fix langevin/eff"_fix_langevin_eff.html "compute temp/eff"_compute_temp_eff.html -"pair eff/cut"_pair_eff.html -"pair eff/inline"_pair_eff.html +"pair_style eff/cut"_pair_eff.html +"pair_style eff/inline"_pair_eff.html examples/USER/eff tools/eff/README tools/eff @@ -2155,11 +2156,47 @@ make machine :pre src/USER-MEAMC: filenames -> commands src/USER-MEAMC/README -"pair meam/c"_pair_meam.html +"pair_style meam/c"_pair_meam.html examples/meam :ul :line +USER-MESO package :link(USER-MESO),h4 + +[Contents:] + +Several extensions of the the dissipative particle dynamics (DPD) +method. Specifically, energy-conserving DPD (eDPD) that can model +non-isothermal processes, many-body DPD (mDPD) for simulating +vapor-liquid coexistence, and transport DPD (tDPD) for modeling +advection-diffuion-reaction systems. The equations of motion of these +DPD extensions are integrated through a modified velocity-Verlet (MVV) +algorithm. + +[Author:] Zhen Li (Division of Applied Mathematics, Brown University) + +[Install or un-install:] + +make yes-user-meso +make machine :pre + +make no-user-meso +make machine :pre + +[Supporting info:] + +src/USER-MESO: filenames -> commands +src/USER-MESO/README +"atom_style edpd"_atom_style.html +"pair_style edpd"_pair_meso.html +"pair_style mdpd"_pair_meso.html +"pair_style tdpd"_pair_meso.html +"fix mvv/dpd"_fix_mvv.html +examples/USER/meso +http://lammps.sandia.gov/movies.html#mesodpd :ul + +:line + USER-MOLFILE package :link(USER-MOLFILE),h4 [Contents:] diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index 077636dfd1..49d9dde791 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -13,17 +13,19 @@ atom_style command :h3 atom_style style args :pre style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \ - {dpd} or {electron} or {ellipsoid} or {full} or {line} or {meso} or \ - {molecular} or {peri} or {smd} or {sphere} or {tri} or \ - {template} or {hybrid} :ulb,l + {dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \ + {full} or {line} or {meso} or {molecular} or {peri} or {smd} or \ + {sphere} or {tri} or {template} or {hybrid} :ulb,l args = none for any style except the following - {body} args = bstyle bstyle-args - bstyle = style of body particles - bstyle-args = additional arguments specific to the bstyle - see the "body"_body.html doc page for details - {template} args = template-ID - template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command - {hybrid} args = list of one or more sub-styles, each with their args :pre + {body} args = bstyle bstyle-args + bstyle = style of body particles + bstyle-args = additional arguments specific to the bstyle + see the "body"_body.html doc page for details + {tdpd} arg = Nspecies + Nspecies = # of chemical species + {template} arg = template-ID + template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command + {hybrid} args = list of one or more sub-styles, each with their args :pre accelerated styles (with same args) = {angle/kk} or {atomic/kk} or {bond/kk} or {charge/kk} or {full/kk} or {molecular/kk} :l :ule @@ -36,7 +38,8 @@ atom_style full atom_style body nparticle 2 10 atom_style hybrid charge bond atom_style hybrid charge body nparticle 2 5 -atom_style template myMols :pre +atom_style template myMols +atom_style tdpd 2 :pre [Description:] @@ -74,6 +77,9 @@ quantities. {charge} | charge | atomic system with charges | {dipole} | charge and dipole moment | system with dipolar particles | {dpd} | internal temperature and internal energies | DPD particles | +{edpd} | temperature and heat capacity | eDPD particles | +{mdpd} | density | mDPD particles | +{tdpd} | chemical concentration | tDPD particles | {electron} | charge and spin and eradius | electronic force field | {ellipsoid} | shape, quaternion, angular momentum | aspherical particles | {full} | molecular + charge | bio-molecules | @@ -145,6 +151,19 @@ properties with internal temperature (dpdTheta), internal conductive energy (uCond), internal mechanical energy (uMech), and internal chemical energy (uChem). +The {edpd} style is for energy-conserving dissipative particle +dynamics (eDPD) particles which store a temperature (edpd_temp), and +heat capacity(edpd_cv). + +The {mdpd} style is for many-body dissipative particle dynamics (mDPD) +particles which store a density (rho) for considering +density-dependent many-body interactions. + +The {tdpd} style is for transport dissipative particle dynamics (tDPD) +particles which store a set of chemical concentration. An integer +"cc_species" is required to specify the number of chemical species +involved in a tDPD system. + The {meso} style is for smoothed particle hydrodynamics (SPH) particles which store a density (rho), energy (e), and heat capacity (cv). @@ -284,6 +303,11 @@ force fields"_pair_eff.html. The {dpd} style is part of the USER-DPD package for dissipative particle dynamics (DPD). +The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package +for energy-conserving dissipative particle dynamics (eDPD), many-body +dissipative particle dynamics (mDPD), and transport dissipative particle +dynamics (tDPD), respectively. + The {meso} style is part of the USER-SPH package for smoothed particle hydrodynamics (SPH). See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff --git a/doc/src/compute_edpd_temp_atom.txt b/doc/src/compute_edpd_temp_atom.txt new file mode 100644 index 0000000000..30f8c1043a --- /dev/null +++ b/doc/src/compute_edpd_temp_atom.txt @@ -0,0 +1,61 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute edpd/temp/atom command :h3 + +[Syntax:] + +compute ID group-ID edpd/temp/atom :pre + +ID, group-ID are documented in "compute"_compute.html command +edpd/temp/atom = style name of this compute command :ul + +[Examples:] + +compute 1 all edpd/temp/atom :pre + +[Description:] + +Define a computation that calculates the per-atom temperature +for each eDPD particle in a group. + +The temperature is a local temperature derived from the internal energy +of each eDPD particle based on the local equilibrium hypothesis. +For more details please see "(Espanol1997)"_#Espanol1997 and "(Li2014)"_#Li2014. + +[Output info:] + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +"Section 6.15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. + +The per-atom vector values will be in temperature "units"_units.html. + +[Restrictions:] + +This compute is part of the USER-MESO package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"pair_style edpd"_pair_meso.html + +[Default:] none + +:line + +:link(Espanol1997) +[(Espanol1997)] Espanol, Europhys Lett, 40(6): 631-636 (1997). DOI: +10.1209/epl/i1997-00515-8 + +:link(Li2014) +[(Li2014)] Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: +113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003. + diff --git a/doc/src/compute_tdpd_cc_atom.txt b/doc/src/compute_tdpd_cc_atom.txt new file mode 100644 index 0000000000..58a49fa59f --- /dev/null +++ b/doc/src/compute_tdpd_cc_atom.txt @@ -0,0 +1,60 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute tdpd/cc/atom command :h3 + +[Syntax:] + +compute ID group-ID tdpd/cc/atom index :pre + +ID, group-ID are documented in "compute"_compute.html command +tdpd/cc/atom = style name of this compute command +index = index of chemical species (1 to Nspecies) :ul + +[Examples:] + +compute 1 all tdpd/cc/atom 2 :pre + +[Description:] + +Define a computation that calculates the per-atom chemical +concentration of a specified species for each tDPD particle in a +group. + +The chemical concentration of each species is defined as the number of +molecules carried by a tDPD particle for dilute solution. For more +details see "(Li2015)"_#Li2015. + +[Output info:] + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +"Section 6.15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. + +The per-atom vector values will be in the units of chemical species +per unit mass. + +[Restrictions:] + +This compute is part of the USER-MESO package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"pair_style tdpd"_pair_meso.html + +[Default:] none + +:line + +:link(Li2015) +[(Li2015)] Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: +014101 (2015). DOI: 10.1063/1.4923254 + diff --git a/doc/src/fix_dpd_source.txt b/doc/src/fix_dpd_source.txt new file mode 100644 index 0000000000..de035a94b4 --- /dev/null +++ b/doc/src/fix_dpd_source.txt @@ -0,0 +1,101 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix edpd/source command :h3 +fix tdpd/source command :h3 + +[Syntax:] + +fix ID group-ID edpd/source keyword values ... +fix ID group-ID tdpd/source cc_index keyword values ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +edpd/source or tdpd/source = style name of this fix command :l +index (only specified for tdpd/source) = index of chemical species (1 to Nspecies) :l +keyword = {sphere} or {cuboid} :l + {sphere} values = cx,cy,cz,radius,source + cx,cy,cz = x,y,z center of spherical domain (distance units) + radius = radius of a spherical domain (distance units) + source = heat source or concentration source (flux units, see below) + {cuboid} values = cx,cy,cz,dLx,dLy,dLz,source + cx,cy,cz = x,y,z lower left corner of a cuboid domain (distance units) + dLx,dLy,dLz = x,y,z side length of a cuboid domain (distance units) + source = heat source or concentration source (flux units, see below) :pre +:ule + +[Examples:] + +fix 1 all edpd/source sphere 0.0 0.0 0.0 5.0 0.01 +fix 1 all edpd/source cuboid 0.0 0.0 0.0 20.0 10.0 10.0 -0.01 +fix 1 all tdpd/source 1 sphere 5.0 0.0 0.0 5.0 0.01 +fix 1 all tdpd/source 2 cuboid 0.0 0.0 0.0 20.0 10.0 10.0 0.01 :pre + +[Description:] + +Fix {edpd/source} adds a heat source as an external heat flux to each +atom in a spherical or cuboid domain, where the {source} is in units +of energy/time. Fix {tdpd/source} adds an external concentration +source of the chemical species specified by {index} as an external +concentration flux for each atom in a spherical or cuboid domain, +where the {source} is in units of mole/volume/time. + +This command can be used to give an additional heat/concentration +source term to atoms in a simulation, such as for a simulation of a +heat conduction with a source term (see Fig.12 in "(Li2014)"_#Li2014) +or diffusion with a source term (see Fig.1 in "(Li2015)"_#Li2015), as +an analog of a periodic Poiseuille flow problem. + +If the {sphere} keyword is used, the {cx,cy,cz,radius} defines a +spherical domain to apply the source flux to. + +If the {cuboid} keyword is used, the {cx,cy,cz,dLx,dLy,dLz} defines a +cuboid domain to apply the source flux to. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various "output +commands"_Section_howto.html#howto_15. No parameter of this fix can +be used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the USER-MESO package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +Fix {edpd/source} must be used with the "pair_style +edpd"_pair_meso.html command. Fix {tdpd/source} must be used with the +"pair_style tdpd"_pair_meso.html command. + +[Related commands:] + +"pair_style edpd"_pair_meso.html, "pair_style tdpd"_pair_meso.html, +"compute edpd/temp/atom"_compute_edpd_temp_atom.html, "compute +tdpd/cc/atom"_compute_tdpd_cc_atom.html + +[Default:] none + +:line + +:link(Li2014) +[(Li2014)] Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis, +"Energy-conserving dissipative particle dynamics with +temperature-dependent properties", J. Comput. Phys., 265: 113-127 +(2014). DOI: 10.1016/j.jcp.2014.02.003 + +:link(Li2015) +[(Li2015)] Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis, +"Transport dissipative particle dynamics model for mesoscopic +advection-diffusion-reaction problems", J. Chem. Phys., 143: 014101 +(2015). DOI: 10.1063/1.4923254 diff --git a/doc/src/fix_mvv_dpd.txt b/doc/src/fix_mvv_dpd.txt new file mode 100644 index 0000000000..75e13744ea --- /dev/null +++ b/doc/src/fix_mvv_dpd.txt @@ -0,0 +1,97 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix mvv/dpd command :h3 +fix mvv/edpd command :h3 +fix mvv/tdpd command :h3 + +[Syntax:] + +fix ID group-ID mvv/dpd lambda :pre +fix ID group-ID mvv/edpd lambda :pre +fix ID group-ID mvv/tdpd lambda :pre + +ID, group-ID are documented in "fix"_fix.html command +mvv/dpd, mvv/edpd, mvv/tdpd = style name of this fix command +lambda = (optional) relaxation parameter (unitless) :ul + +[Examples:] + +fix 1 all mvv/dpd +fix 1 all mvv/dpd 0.5 +fix 1 all mvv/edpd +fix 1 all mvv/edpd 0.5 +fix 1 all mvv/tdpd +fix 1 all mvv/tdpd 0.5 :pre + +[Description:] + +Perform time integration using the modified velocity-Verlet (MVV) +algorithm to update position and velocity (fix mvv/dpd), or position, +velocity and temperature (fix mvv/edpd), or position, velocity and +concentration (fix mvv/tdpd) for particles in the group each timestep. + +The modified velocity-Verlet (MVV) algorithm aims to improve the +stability of the time integrator by using an extrapolated version of +the velocity for the force evaluation: + +:c,image(Eqs/fix_mvv_dpd.jpg) + +where the parameter λ depends on the +specific choice of DPD parameters, and needs to be tuned on a +case-by-case basis. Specification of a {lambda} value is opttional. +If specified, the setting must be from 0.0 to 1.0. If not specified, +a default value of 0.5 is used, which effectively reproduces the +standard velocity-Verlet (VV) scheme. For more details, see +"Groot"_#Groot. + +Fix {mvv/dpd} updates the position and velocity of each atom. It can +be used with the "pair_style mdpd"_pair_meso.html command or other +pair styles such as "pair dpd"_pair_dpd.html. + +Fix {mvv/edpd} updates the per-atom temperature, in addition to +position and velocity, and must be used with the "pair_style +edpd"_pair_meso.html command. + +Fix {mvv/tdpd} updates the per-atom chemical concentration, in +addition to position and velocity, and must be used with the +"pair_style tdpd"_pair_meso.html command. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various "output +commands"_Section_howto.html#howto_15. No parameter of this fix can +be used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the USER-MESO package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"pair_style mdpd"_pair_meso.html, "pair_style edpd"_pair_meso.html, +"pair_style tdpd"_pair_meso.html + +[Default:] + +The default value for the optional {lambda} parameter is 0.5. + +:line + +:link(Groot) +[(Groot)] Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI: +10.1063/1.474784 + diff --git a/doc/src/pair_meso.txt b/doc/src/pair_meso.txt new file mode 100644 index 0000000000..bcdf717d68 --- /dev/null +++ b/doc/src/pair_meso.txt @@ -0,0 +1,277 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style edpd command :h3 +pair_style mdpd command :h3 +pair_style mdpd/rhosum command :h3 +pair_style tdpd command :h3 + +[Syntax:] + +pair_style style args :pre + +style = {edpd} or {mdpd} or {mdpd/rhosum} or {tdpd} :ulb,l +args = list of arguments for a particular style :l + {edpd} args = cutoff seed + cutoff = global cutoff for eDPD interactions (distance units) + seed = random # seed (integer) (if <= 0, eDPD will use current time as the seed) + {mdpd} args = T cutoff seed + T = temperature (temperature units) + cutoff = global cutoff for mDPD interactions (distance units) + seed = random # seed (integer) (if <= 0, mDPD will use current time as the seed) + {mdpd/rhosum} args = + {tdpd} args = T cutoff seed + T = temperature (temperature units) + cutoff = global cutoff for tDPD interactions (distance units) + seed = random # seed (integer) (if <= 0, tDPD will use current time as the seed) :pre +:ule + +[Examples:] + +pair_style edpd 1.58 9872598 +pair_coeff * * 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 +pair_coeff 1 1 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 +pair_coeff 1 1 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00 :pre + +pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 65689 +pair_coeff 1 1 mdpd/rhosum 0.75 +pair_coeff 1 1 mdpd -40.0 25.0 18.0 1.0 0.75 :pre + +pair_style tdpd 1.0 1.58 935662 +pair_coeff * * 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 +pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 :pre + +[Description:] + +The {edpd} style computes the pairwise interactions and heat fluxes +for eDPD particles following the formulations in +"(Li2014_JCP)"_#Li2014_JCP and "Li2015_CC"_#Li2015_CC. The time +evolution of an eDPD particle is governed by the conservation of +momentum and energy given by + +:c,image(Eqs/pair_edpd_gov.jpg) + +where the three components of Fi +including the conservative force FijC, dissipative force FijD and random force FijR are expressed as + +:c,image(Eqs/pair_edpd_force.jpg) + +in which the exponent of the weighting function s can be defined as a temperature-dependent +variable. The heat flux between particles accounting for the +collisional heat flux qC, viscous +heat flux qV, and random heat flux +qR are given by + +:c,image(Eqs/pair_edpd_heat.jpg) + +where the mesoscopic heat friction κ is given by + +:c,image(Eqs/pair_edpd_kappa.jpg) + +with υ being the kinematic +viscosity. For more details, see Eq.(15) in "(Li2014_JCP)"_#Li2014_JCP. + +The following coefficients must be defined in eDPD system for each +pair of atom types via the "pair_coeff"_pair_coeff.html command as in +the examples above. + +A (force units) +gamma (force/velocity units) +power_f (positive real) +cutoff (distance units) +kappa (thermal conductivity units) +power_T (positive real) +cutoff_T (distance units) +optional keyword = power or kappa :ul + +The keyword {power} or {kappa} is optional. Both "power" and "kappa" +require 4 parameters c1, c2, +c4, c4 showing the temperature dependence +of the exponent
s(T) = +power_f*(1+c1*(T-1)+c2*(T-1)2 ++c3*(T-1)3+c4*(T-1)4)
+and of the mesoscopic heat friction
+sT(T) = +kappa*(1+c1*(T-1)+c2*(T-1)2 ++c3*(T-1)3+c4*(T-1)4)
+If the keyword {power} or {kappa} is not specified, the eDPD system +will use constant power_f and kappa, which is independent to +temperature changes. + +:line + +The {mdpd/rhosum} style computes the local particle mass density rho +for mDPD particles by kernel function interpolation. + +The following coefficients must be defined for each pair of atom types +via the "pair_coeff"_pair_coeff.html command as in the examples above. + +cutoff (distance units) :ul + +:line + +The {mdpd} style computes the many-body interactions between mDPD +particles following the formulations in +"(Li2013_POF)"_#Li2013_POF. The dissipative and random forces are in +the form same as the classical DPD, but the conservative force is +local density dependent, which are given by + +:c,image(Eqs/pair_mdpd_force.jpg) + +where the first term in FC with a +negative coefficient A < 0 stands for an attractive force within an +interaction range rc, and the second +term with B > 0 is the density-dependent repulsive force within an +interaction range rd. + +The following coefficients must be defined for each pair of atom types via the +"pair_coeff"_pair_coeff.html command as in the examples above. + +A (force units) +B (force units) +gamma (force/velocity units) +cutoff_c (distance units) +cutoff_d (distance units) :ul + +:line + +The {tdpd} style computes the pairwise interactions and chemical +concentration fluxes for tDPD particles following the formulations in +"(Li2015_JCP)"_#Li2015_JCP. The time evolution of a tDPD particle is +governed by the conservation of momentum and concentration given by + +:c,image(Eqs/pair_tdpd_gov.jpg) + +where the three components of Fi +including the conservative force FijC, dissipative force FijD and random force FijR are expressed as + +:c,image(Eqs/pair_tdpd_force.jpg) + +The concentration flux between two tDPD particles includes the Fickian +flux QijD and random flux +QijR, which are given by + +:c,image(Eqs/pair_tdpd_flux.jpg) + +where the parameters kappa and epsilon determine the strength of the +Fickian and random fluxes. ms +is the mass of a single solute molecule. In general, ms is much smaller than the mass of +a tDPD particle m. For more details, see +"(Li2015_JCP)"_#Li2015_JCP. + +The following coefficients must be defined for each pair of atom types via the +"pair_coeff"_pair_coeff.html command as in the examples above. + +A (force units) +gamma (force/velocity units) +power_f (positive real) +cutoff (distance units) +cutoff_CC (distance units) +kappa_i (diffusivity units) +epsilon_i (diffusivity units) +power_cc_i (positive real) :ul + +The last 3 values must be repeated Nspecies times, so that values for +each of the Nspecies chemical species are specified, as indicated by +the "I" suffix. In the first pair_coeff example above for pair_style +tdpd, Nspecies = 1. In the second example, Nspecies = 2, so 3 +additional coeffs are specified (for species 2). + +:line + +[Example scripts] + +There are example scripts for using all these pair styles in +examples/USER/meso. The example for an eDPD simulation models heat +conduction with source terms analog of periodic Poiseuille flow +problem. The setup follows Fig.12 in "(Li2014_JCP)"_#Li2014_JCP. The +output of the short eDPD simulation (about 2 minutes on a single core) +gives a temperature and density profiles as + +:c,image(JPG/examples_edpd.jpg) + +The example for a mDPD simulation models the oscillations of a liquid +droplet started from a liquid film. The mDPD parameters are adopted +from "(Li2013_POF)"_#Li2013_POF. The short mDPD run (about 2 minutes +on a single core) generates a particle trajectory which can +be visualized as follows. + +:c,image(JPG/examples_mdpd_first.jpg,JPG/examples_mdpd.gif) +:c,image(JPG/examples_mdpd_last.jpg) + +The first image is the initial state of the simulation. If you +click it a GIF movie should play in your browser. The second image +is the final state of the simulation. + +The example for a tDPD simulation computes the effective diffusion +coefficient of a tDPD system using a method analogous to the periodic +Poiseuille flow. The tDPD system is specified with two chemical +species, and the setup follows Fig.1 in +"(Li2015_JCP)"_#Li2015_JCP. The output of the short tDPD simulation +(about one and a half minutes on a single core) gives the +concentration profiles of the two chemical species as + +:c,image(JPG/examples_tdpd.jpg) + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +The styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} do not support +mixing. Thus, coefficients for all I,J pairs must be specified explicitly. + +The styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} do not support +the "pair_modify"_pair_modify.html shift, table, and tail options. + +The styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} do not write +information to "binary restart files"_restart.html. Thus, you need +to re-specify the pair_style and pair_coeff commands in an input script +that reads a restart file. + +[Restrictions:] + +The pair styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} are part of +the USER-MESO package. It is only enabled if LAMMPS was built with +that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, "fix mvv/dpd"_fix_mvv_dpd.html, +"fix mvv/edpd"_fix_mvv_dpd.html, "fix mvv/tdpd"_fix_mvv_dpd.html, +"fix edpd/source"_fix_dpd_source.html, "fix tdpd/source"_fix_dpd_source.html, +"compute edpd/temp/atom"_compute_edpd_temp_atom.html, +"compute tdpd/cc/atom"_compute_tdpd_cc_atom.html + +[Default:] none + +:line + +:link(Li2014_JCP) +[(Li2014_JCP)] Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, +265: 113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003. + +:link(Li2015_CC) +[(Li2015_CC)] Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 +(2015). DOI: 10.1039/C5CC01684C. + +:link(Li2013_POF) +[(Li2013_POF)] Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). +DOI: 10.1063/1.4812366. + +:link(Li2015_JCP) +[(Li2015_JCP)] Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, +143: 014101 (2015). DOI: 10.1063/1.4923254. diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index a8aca53693..747c3e752d 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -14,7 +14,7 @@ read_data file keyword args ... :pre file = name of data file to read in :ulb,l zero or more keyword/arg pairs may be appended :l -keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/types} or {extra/angle/types} or {extra/dihedral/types} or {extra/improper/types} or {extra/bond/per/atom} or {extra/angle/per/atom} or {extra/dihedral/per/atom} or {extra/improper/per/atom} or {group} or {nocoeff} or {fix} :l +keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/types} or {extra/angle/types} or {extra/dihedral/types} or {extra/improper/types} or {group} or {nocoeff} or {fix} :l {add} arg = {append} or {Nstart} or {merge} append = add new atoms with IDs appended to current IDs Nstart = add new atoms with IDs starting with Nstart @@ -32,11 +32,6 @@ keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/type {extra/angle/types} arg = # of extra angle types {extra/dihedral/types} arg = # of extra dihedral types {extra/improper/types} arg = # of extra improper types - {extra/bond/per/atom} arg = leave space for this many new bonds per atom - {extra/angle/per/atom} arg = leave space for this many new angles per atom - {extra/dihedral/per/atom} arg = leave space for this many new dihedrals per atom - {extra/improper/per/atom} arg = leave space for this many new impropers per atom - {extra/special/per/atom} arg = leave space for extra 1-2,1-3,1-4 interactions per atom {group} args = groupID groupID = add atoms in data file to this group {nocoeff} = ignore force field parameters @@ -62,7 +57,7 @@ simulation. The file can be ASCII text or a gzipped text file atom coordinates; see the "read_restart"_read_restart.html and "create_atoms"_create_atoms.html commands for alternative methods. Also see the explanation of the "-restart command-line -switch"_Section_start.html#start_6 which can convert a restart file to +switch"_Section_start.html#start_7 which can convert a restart file to a data file. This command can be used multiple times to add new atoms and their @@ -269,11 +264,11 @@ is different than the default. {angle types} = # of angle types in system {dihedral types} = # of dihedral types in system {improper types} = # of improper types in system -{extra bond per atom} = leave space for this many new bonds per atom (deprecated, use extra/bond/per/atom keyword) -{extra angle per atom} = leave space for this many new angles per atom (deprecated, use extra/angle/per/atom keyword) -{extra dihedral per atom} = leave space for this many new dihedrals per atom (deprecated, use extra/dihedral/per/atom keyword) -{extra improper per atom} = leave space for this many new impropers per atom (deprecated, use extra/improper/per/atom keyword) -{extra special per atom} = leave space for this many new special bonds per atom (deprecated, use extra/special/per/atom keyword) +{extra bond per atom} = leave space for this many new bonds per atom +{extra angle per atom} = leave space for this many new angles per atom +{extra dihedral per atom} = leave space for this many new dihedrals per atom +{extra improper per atom} = leave space for this many new impropers per atom +{extra special per atom} = leave space for this many new special bonds per atom {ellipsoids} = # of ellipsoids in system {lines} = # of line segments in system {triangles} = # of triangles in system @@ -372,32 +367,25 @@ read_data command will generate an error in this case. The "extra bond per atom" setting (angle, dihedral, improper) is only needed if new bonds (angles, dihedrals, impropers) will be added to the system when a simulation runs, e.g. by using the "fix -bond/create"_fix_bond_create.html command. Using this header flag -is deprecated; please use the {extra/bond/per/atom} keyword (and -correspondingly for angles, dihedrals and impropers) in the -read_data command instead. Either will pre-allocate space in LAMMPS - data structures for storing the new bonds (angles, +bond/create"_fix_bond_create.html command. This will pre-allocate +space in LAMMPS data structures for storing the new bonds (angles, dihedrals, impropers). The "extra special per atom" setting is typically only needed if new bonds/angles/etc will be added to the system, e.g. by using the "fix bond/create"_fix_bond_create.html command. Or if entire new molecules -will be added to the system, e.g. by using the -"fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands, -which will have more special 1-2,1-3,1-4 neighbors than any other -molecules defined in the data file. Using this header flag is -deprecated; please use the {extra/special/per/atom} keyword instead. -Using this setting will pre-allocate space in the LAMMPS data -structures for storing these neighbors. See the +will be added to the system, e.g. by using the "fix +deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands, which +will have more special 1-2,1-3,1-4 neighbors than any other molecules +defined in the data file. Using this setting will pre-allocate space +in the LAMMPS data structures for storing these neighbors. See the "special_bonds"_special_bonds.html and "molecule"_molecule.html doc pages for more discussion of 1-2,1-3,1-4 neighbors. -NOTE: All of the "extra" settings are only applied in the first data -file read and when no simulation box has yet been created; as soon as -the simulation box is created (and read_data implies that), these -settings are {locked} and cannot be changed anymore. Please see the -description of the {add} keyword above for reading multiple data files. -If they appear in later data files, they are ignored. +NOTE: All of the "extra" settings are only used if they appear in the +first data file read; see the description of the {add} keyword above +for reading multiple data files. If they appear in later data files, +they are ignored. The "ellipsoids" and "lines" and "triangles" and "bodies" settings are only used with "atom_style ellipsoid or line or tri or @@ -547,6 +535,9 @@ bond: atom-ID molecule-ID atom-type x y z charge: atom-ID atom-type q x y z dipole: atom-ID atom-type q x y z mux muy muz dpd: atom-ID atom-type theta x y z +edpd: atom-ID atom-type edpd_temp edpd_cv x y z +mdpd: atom-ID atom-type x y z +tdpd: atom-ID atom-type x y z cc1 cc2 ... ccNspecies electron: atom-ID atom-type q spin eradius x y z ellipsoid: atom-ID atom-type ellipsoidflag density x y z full: atom-ID molecule-ID atom-type q x y z @@ -566,12 +557,15 @@ The per-atom values have these meanings and units, listed alphabetically: atom-ID = integer ID of atom atom-type = type of atom (1-Ntype) bodyflag = 1 for body particles, 0 for point particles +cc = chemical concentration for tDPD particles for each species (mole/volume units) contact-radius = ??? (distance units) cs_re,cs_im = real/imaginary parts of wavepacket coefficients cv = heat capacity (need units) for SPH particles density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle) diameter = diameter of spherical atom (distance units) e = energy (need units) for SPH particles +edpd_temp = temperature for eDPD particles (temperature units) +edpd_cv = volumetric heat capacity for eDPD particles (energy/temperature/volume units) ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles eradius = electron radius (or fixed-core radius) etag = integer ID of electron that each wavepacket belongs to diff --git a/doc/src/set.txt b/doc/src/set.txt index 14460c9741..4757d1c575 100644 --- a/doc/src/set.txt +++ b/doc/src/set.txt @@ -24,7 +24,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ {bond} or {angle} or {dihedral} or {improper} or \ {meso/e} or {meso/cv} or {meso/rho} or \ {smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \ - {i_name} or {d_name} :l + {edpd/temp} or {edpd/cv} or {cc} or {i_name} or {d_name} :l {type} value = atom type value can be an atom-style variable (see below) {type/fraction} values = type fraction seed @@ -98,6 +98,13 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ {dpd/theta} value = internal temperature of DPD particles (temperature units) value can be an atom-style variable (see below) value can be NULL which sets internal temp of each particle to KE temp + {edpd/temp} value = temperature of eDPD particles (temperature units) + value can be an atom-style variable (see below) + {edpd/cv} value = volumetric heat capacity of eDPD particles (energy/temperature/volume units) + value can be an atom-style variable (see below) + {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 :pre :ule @@ -418,6 +425,19 @@ value >= 0.0, the internal temperature is set to that value. If it is < 0.0, the computation of Tkin is performed and the internal temperature is set to that value. +Keywords {edpd/temp} and {edpd/cv} set the temperature and volumetric +heat capacity of an eDPD particle as defined by the USER-MESO package. +Currently, only "atom_style edpd"_atom_style.html defines particles +with these attributes. The values for the temperature and heat +capacity must be positive. + +Keyword {cc} sets the chemical concentration of a tDPD particle for a +specified species as defined by the USER-MESO package. Currently, only +"atom_style tdpd"_atom_style.html defines particles with this +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 "fix property/atom"_fix_property_atom.html command. When that command diff --git a/examples/USER/meso/README b/examples/USER/meso/README new file mode 100644 index 0000000000..4accc7ba01 --- /dev/null +++ b/examples/USER/meso/README @@ -0,0 +1,40 @@ +This directory contains input scripts for performing +simulations with these models: + +eDPD - energy-conserving dissipative particle dynamics +mDPD - many-body dissipative particle dynamics +tDPD - transport dissipative particle dynamics + +1) eDPD: The input script in.mdpd is an example simulation of +measuring the thermal conductivity by heat conduction analog of +periodic Poiseuille flow. The initial eDPD system is randomly filled +by many eDPD particles, and a set command "edpd/temp" gives the +initial temperature and a set command "edpd/cv" gives the heat +capacity of eDPD particles. A non-contact heat source/sink term is +applied by a fix command "edpd/source". A compute command +"edpd/temp/atom" obtain the temperature on each eDPD particle. The +simulation will generate a file named "temp.profile" showing the +temperature profile. For details please see online LAMMPS +documentation and Fig.12 in the paper Z. Li, et al. J Comput Phys, +2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 + +2) mDPD: The input script "in.mdpd" is an example simulation of +oscillations of a free liquid droplet. The initial configuration is a +liquid film whose particles are in a fcc lattice created by the +command "create atoms". Then the liquid film has a tendency to form a +spherical droplet under the effect of surface tension. For details +please see online LAMMPS documentation and the paper Z. Li, et +al. Phys Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 + +3) tDPD: The input script in.tdpd is an example simulation of +computing the effective diffusion coefficient of a tDPD system using a +method analogous to the periodic Poiseuille flow. Command "atom_style +tdpd 2" specifies the tDPD system with two chemical species. The +initial tDPD system is randomly filled by many tDPD particles, and a +set "cc" command gives initial concentration for each chemical +species. Fix commands "tdpd/source" add source terms and compute +commands "tdpd/cc/atom" obtain the chemical concentration on each tDPD +particle. The simulation will generate a file named "cc.profile" +showing the concentration profiles of the two chemical species. For +details please see online LAMMPS documentation and Fig.1 in the paper +Z. Li, et al. J Chem Phys, 2015, 143: 014101. DOI: 10.1063/1.4923254 diff --git a/examples/USER/meso/edpd/in.edpd b/examples/USER/meso/edpd/in.edpd new file mode 100644 index 0000000000..316099bce3 --- /dev/null +++ b/examples/USER/meso/edpd/in.edpd @@ -0,0 +1,54 @@ +######################################################################## +### Heat conduction analog of periodic Poiseuille flow problem ### +### using energy-conserving DPD (eDPD) simulation ### +### ### +### Created : Zhen Li (zhen_li@brown.edu) ### +### Division of Applied Mathematics, Brown University. ### +### ### +### mDPD system setup follows Fig.12 in the publication: ### +### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ### +### "Energy-conserving dissipative particle dynamics with ### +### temperature-dependent properties". J. Comput. Phys., ### +### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes + +atom_style edpd + +region edpd block -10 10 -10 10 -5 5 units box +create_box 1 edpd +create_atoms 1 random 16000 276438 NULL +mass 1 1.0 +set atom * edpd/temp 1.0 +set atom * edpd/cv 1.0E5 + +pair_style edpd 1.58 9872598 +#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58 +pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 & + power 10.54 -3.66 3.44 -4.10 & + kappa -0.44 -3.21 5.04 0.00 + +compute mythermo all temp +thermo 100 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 432982 loop local dist gaussian + +fix mvv all mvv/edpd 0.5 +fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 +fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 + +timestep 0.01 +run 500 +reset_timestep 0 + +compute temp all edpd/temp/atom +compute ccT all chunk/atom bin/1d y 0.0 1.0 +fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile + +run 500 diff --git a/examples/USER/meso/edpd/log.16Aug17.edpd.g++.1 b/examples/USER/meso/edpd/log.16Aug17.edpd.g++.1 new file mode 100644 index 0000000000..af975f877c --- /dev/null +++ b/examples/USER/meso/edpd/log.16Aug17.edpd.g++.1 @@ -0,0 +1,142 @@ +LAMMPS (11 Aug 2017) +######################################################################## +### Heat conduction analog of periodic Poiseuille flow problem ### +### using energy-conserving DPD (eDPD) simulation ### +### ### +### Created : Zhen Li (zhen_li@brown.edu) ### +### Division of Applied Mathematics, Brown University. ### +### ### +### mDPD system setup follows Fig.12 in the publication: ### +### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ### +### "Energy-conserving dissipative particle dynamics with ### +### temperature-dependent properties". J. Comput. Phys., ### +### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes + +atom_style edpd + +region edpd block -10 10 -10 10 -5 5 units box +create_box 1 edpd +Created orthogonal box = (-10 -10 -5) to (10 10 5) + 1 by 1 by 1 MPI processor grid +create_atoms 1 random 16000 276438 NULL +Created 16000 atoms +mass 1 1.0 +set atom * edpd/temp 1.0 + 16000 settings made for edpd/temp +set atom * edpd/cv 1.0E5 + 16000 settings made for edpd/cv + +pair_style edpd 1.58 9872598 +#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58 +pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00 + +compute mythermo all temp +thermo 100 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 432982 loop local dist gaussian + +fix mvv all mvv/edpd 0.5 +fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 +fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 + +timestep 0.01 +run 500 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.78 + ghost atom cutoff = 1.78 + binsize = 0.89, bins = 23 23 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair edpd, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.64 | 11.64 | 11.64 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1 48.948932 0 50.448838 201.73366 + 100 1.0069712 43.754293 0 45.264656 199.5369 + 200 0.98667561 43.716052 0 45.195973 196.72854 + 300 1.0036944 43.706299 0 45.211746 195.35714 + 400 1.0024228 43.697014 0 45.200554 197.0062 + 500 0.99968161 43.687445 0 45.186873 193.80596 +Loop time of 80.7995 on 1 procs for 500 steps with 16000 atoms + +Performance: 5346.567 tau/day, 6.188 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 75.106 | 75.106 | 75.106 | 0.0 | 92.95 +Neigh | 4.9836 | 4.9836 | 4.9836 | 0.0 | 6.17 +Comm | 0.31199 | 0.31199 | 0.31199 | 0.0 | 0.39 +Output | 0.00048232 | 0.00048232 | 0.00048232 | 0.0 | 0.00 +Modify | 0.29985 | 0.29985 | 0.29985 | 0.0 | 0.37 +Other | | 0.09751 | | | 0.12 + +Nlocal: 16000 ave 16000 max 16000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 14091 ave 14091 max 14091 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 749111 ave 749111 max 749111 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 749111 +Ave neighs/atom = 46.8194 +Neighbor list builds = 181 +Dangerous builds = 0 +reset_timestep 0 + +compute temp all edpd/temp/atom +compute ccT all chunk/atom bin/1d y 0.0 1.0 +fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile + +run 500 +Per MPI rank memory allocation (min/avg/max) = 12.14 | 12.14 | 12.14 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.99968161 43.687397 0 45.186825 196.38426 + 100 1.0041443 43.668196 0 45.174318 195.38066 + 200 0.99628392 43.666173 0 45.160505 197.84675 + 300 1.0029116 43.66224 0 45.166513 199.67414 + 400 0.99922193 43.64406 0 45.142799 196.94404 + 500 0.99355431 43.623266 0 45.113505 195.94136 +Loop time of 80.7742 on 1 procs for 500 steps with 16000 atoms + +Performance: 5348.242 tau/day, 6.190 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 75.073 | 75.073 | 75.073 | 0.0 | 92.94 +Neigh | 4.8786 | 4.8786 | 4.8786 | 0.0 | 6.04 +Comm | 0.31086 | 0.31086 | 0.31086 | 0.0 | 0.38 +Output | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.00 +Modify | 0.4139 | 0.4139 | 0.4139 | 0.0 | 0.51 +Other | | 0.09731 | | | 0.12 + +Nlocal: 16000 ave 16000 max 16000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 14091 ave 14091 max 14091 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 749667 ave 749667 max 749667 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 749667 +Ave neighs/atom = 46.8542 +Neighbor list builds = 178 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:02:41 diff --git a/examples/USER/meso/edpd/log.16Aug17.edpd.g++.4 b/examples/USER/meso/edpd/log.16Aug17.edpd.g++.4 new file mode 100644 index 0000000000..21206d38c6 --- /dev/null +++ b/examples/USER/meso/edpd/log.16Aug17.edpd.g++.4 @@ -0,0 +1,142 @@ +LAMMPS (11 Aug 2017) +######################################################################## +### Heat conduction analog of periodic Poiseuille flow problem ### +### using energy-conserving DPD (eDPD) simulation ### +### ### +### Created : Zhen Li (zhen_li@brown.edu) ### +### Division of Applied Mathematics, Brown University. ### +### ### +### mDPD system setup follows Fig.12 in the publication: ### +### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ### +### "Energy-conserving dissipative particle dynamics with ### +### temperature-dependent properties". J. Comput. Phys., ### +### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes + +atom_style edpd + +region edpd block -10 10 -10 10 -5 5 units box +create_box 1 edpd +Created orthogonal box = (-10 -10 -5) to (10 10 5) + 2 by 2 by 1 MPI processor grid +create_atoms 1 random 16000 276438 NULL +Created 16000 atoms +mass 1 1.0 +set atom * edpd/temp 1.0 + 16000 settings made for edpd/temp +set atom * edpd/cv 1.0E5 + 16000 settings made for edpd/cv + +pair_style edpd 1.58 9872598 +#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58 +pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00 + +compute mythermo all temp +thermo 100 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 432982 loop local dist gaussian + +fix mvv all mvv/edpd 0.5 +fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 +fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 + +timestep 0.01 +run 500 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.78 + ghost atom cutoff = 1.78 + binsize = 0.89, bins = 23 23 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair edpd, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.969 | 4.979 | 4.985 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1 48.948932 0 50.448838 199.51547 + 100 1.0106415 43.744371 0 45.260239 196.39598 + 200 1.0053215 43.714413 0 45.222301 195.35298 + 300 0.99886399 43.713356 0 45.211559 196.74821 + 400 1.0035264 43.699086 0 45.204282 195.47446 + 500 1.0025285 43.698051 0 45.20175 197.27042 +Loop time of 21.165 on 4 procs for 500 steps with 16000 atoms + +Performance: 20411.046 tau/day, 23.624 timesteps/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 18.713 | 19.101 | 19.41 | 6.0 | 90.25 +Neigh | 1.2687 | 1.2925 | 1.3177 | 1.5 | 6.11 +Comm | 0.33013 | 0.66337 | 1.0747 | 34.3 | 3.13 +Output | 0.00023484 | 0.00028092 | 0.00036526 | 0.0 | 0.00 +Modify | 0.073931 | 0.075277 | 0.076306 | 0.3 | 0.36 +Other | | 0.03227 | | | 0.15 + +Nlocal: 4000 ave 4067 max 3930 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 5997.5 ave 6052 max 5943 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 187388 ave 193157 max 181221 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 749552 +Ave neighs/atom = 46.847 +Neighbor list builds = 181 +Dangerous builds = 0 +reset_timestep 0 + +compute temp all edpd/temp/atom +compute ccT all chunk/atom bin/1d y 0.0 1.0 +fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile + +run 500 +Per MPI rank memory allocation (min/avg/max) = 5.221 | 5.23 | 5.236 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.0025285 43.69801 0 45.201708 194.00452 + 100 0.9885969 43.679927 0 45.16273 196.28442 + 200 1.0028463 43.663067 0 45.167242 198.25592 + 300 1.0027516 43.648817 0 45.152851 198.82226 + 400 0.99695312 43.641469 0 45.136805 197.97499 + 500 0.98202292 43.627163 0 45.100105 199.16319 +Loop time of 21.576 on 4 procs for 500 steps with 16000 atoms + +Performance: 20022.203 tau/day, 23.174 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 18.438 | 19.121 | 19.812 | 14.1 | 88.62 +Neigh | 1.2568 | 1.2885 | 1.325 | 2.5 | 5.97 +Comm | 0.29482 | 1.0219 | 1.7352 | 63.9 | 4.74 +Output | 0.00027728 | 0.00029719 | 0.0003531 | 0.0 | 0.00 +Modify | 0.11153 | 0.11265 | 0.1135 | 0.2 | 0.52 +Other | | 0.03194 | | | 0.15 + +Nlocal: 4000 ave 4092 max 3899 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5974 ave 6019 max 5915 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 187414 ave 196149 max 178418 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 749658 +Ave neighs/atom = 46.8536 +Neighbor list builds = 181 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:42 diff --git a/examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.1 b/examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.1 new file mode 100644 index 0000000000..469b550258 --- /dev/null +++ b/examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.1 @@ -0,0 +1,24 @@ +# Chunk-averaged data for fix stat and group density/number +# Timestep Number-of-chunks Total-count +# Chunk Coord1 Ncount c_temp density/number +500 20 16000 + 1 -9.5 801.636 0.986368 4.00818 + 2 -8.5 809.788 0.966281 4.04894 + 3 -7.5 819.754 0.952764 4.09877 + 4 -6.5 820.364 0.944592 4.10182 + 5 -5.5 826.146 0.940968 4.13073 + 6 -4.5 819.52 0.941415 4.0976 + 7 -3.5 815.182 0.945887 4.07591 + 8 -2.5 817.168 0.95487 4.08584 + 9 -1.5 817.282 0.969225 4.08641 + 10 -0.5 804.204 0.989552 4.02102 + 11 0.5 793.266 1.01015 3.96633 + 12 1.5 789.056 1.0308 3.94528 + 13 2.5 784.344 1.04568 3.92172 + 14 3.5 780.592 1.05508 3.90296 + 15 4.5 772.218 1.05968 3.86109 + 16 5.5 776.968 1.06003 3.88484 + 17 6.5 780.858 1.05612 3.90429 + 18 7.5 786.174 1.04752 3.93087 + 19 8.5 788.922 1.03347 3.94461 + 20 9.5 796.558 1.01278 3.98279 diff --git a/examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.4 b/examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.4 new file mode 100644 index 0000000000..1c50a9b6e5 --- /dev/null +++ b/examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.4 @@ -0,0 +1,24 @@ +# Chunk-averaged data for fix stat and group density/number +# Timestep Number-of-chunks Total-count +# Chunk Coord1 Ncount c_temp density/number +500 20 16000 + 1 -9.5 801.642 0.986089 4.00821 + 2 -8.5 819.168 0.966072 4.09584 + 3 -7.5 817.382 0.952718 4.08691 + 4 -6.5 818 0.944633 4.09 + 5 -5.5 817.806 0.941105 4.08903 + 6 -4.5 826.11 0.941499 4.13055 + 7 -3.5 821.946 0.945922 4.10973 + 8 -2.5 816.202 0.954889 4.08101 + 9 -1.5 813.202 0.969281 4.06601 + 10 -0.5 798.904 0.989463 3.99452 + 11 0.5 798.056 1.01005 3.99028 + 12 1.5 793.114 1.03073 3.96557 + 13 2.5 782.812 1.04569 3.91406 + 14 3.5 775.69 1.05498 3.87845 + 15 4.5 778.094 1.05965 3.89047 + 16 5.5 778.856 1.06002 3.89428 + 17 6.5 780.51 1.05621 3.90255 + 18 7.5 780.518 1.04782 3.90259 + 19 8.5 789.698 1.03348 3.94849 + 20 9.5 792.29 1.01261 3.96145 diff --git a/examples/USER/meso/mdpd/in.mdpd b/examples/USER/meso/mdpd/in.mdpd new file mode 100644 index 0000000000..201b4a340e --- /dev/null +++ b/examples/USER/meso/mdpd/in.mdpd @@ -0,0 +1,52 @@ +######################################################################## +#### 3D droplet oscilation using many-body DPD simulation ### +#### ### +#### Created : Zhen Li (zhen_li@brown.edu) ### +#### Division of Applied Mathematics, Brown University. ### +#### ### +#### mDPD parameters follow the choice of the publication: ### +#### Z. Li et al. "Three dimensional flow structures in a moving ### +#### droplet on substrate: a dissipative particle dynamics study" ### +#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.3 bin +neigh_modify every 1 delay 0 check yes + +atom_style mdpd + +region mdpd block -25 25 -10 10 -10 10 units box +create_box 1 mdpd + +lattice fcc 6 +region film block -20 20 -7.5 7.5 -2.0 2.0 units box +create_atoms 1 region film + +pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598 +pair_coeff 1 1 mdpd/rhosum 0.75 +pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75 +mass 1 1.0 + +compute mythermo all temp +thermo 100 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 38497 loop local dist gaussian + +fix mvv all mvv/dpd + +#dump mydump all atom 100 atom.lammpstrj + +#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 & +# view 90 90 box no 0 size 600 200 +#dump_modify jpg pad 4 + +#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 & +# view 90 90 box no 0 size 600 200 +#dump_modify avi pad 4 + +timestep 0.01 +run 4000 diff --git a/examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.1 b/examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.1 new file mode 100644 index 0000000000..c3c14da559 --- /dev/null +++ b/examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.1 @@ -0,0 +1,147 @@ +LAMMPS (11 Aug 2017) +######################################################################## +#### 3D droplet oscilation using many-body DPD simulation ### +#### ### +#### Created : Zhen Li (zhen_li@brown.edu) ### +#### Division of Applied Mathematics, Brown University. ### +#### ### +#### mDPD parameters follow the choice of the publication: ### +#### Z. Li et al. "Three dimensional flow structures in a moving ### +#### droplet on substrate: a dissipative particle dynamics study" ### +#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.3 bin +neigh_modify every 1 delay 0 check yes + +atom_style mdpd + +region mdpd block -25 25 -10 10 -10 10 units box +create_box 1 mdpd +Created orthogonal box = (-25 -10 -10) to (25 10 10) + 1 by 1 by 1 MPI processor grid + +lattice fcc 6 +Lattice spacing in x,y,z = 0.87358 0.87358 0.87358 +region film block -20 20 -7.5 7.5 -2.0 2.0 units box +create_atoms 1 region film +Created 14333 atoms + +pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598 +pair_coeff 1 1 mdpd/rhosum 0.75 +pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75 +mass 1 1.0 + +compute mythermo all temp +thermo 100 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 38497 loop local dist gaussian + +fix mvv all mvv/dpd + +dump mydump all atom 100 atom.lammpstrj + +#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 # view 90 90 box no 0 size 600 200 +#dump_modify jpg pad 4 + +#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 # view 90 90 box no 0 size 600 200 +#dump_modify avi pad 4 + +timestep 0.01 +run 4000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 77 31 31 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair mdpd/rhosum, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair mdpd, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.931 | 9.931 | 9.931 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1 -13.346542 0 -11.846647 -6.8495478 + 100 1.0321029 -7.2846779 0 -5.7366316 -0.77640205 + 200 1.042287 -6.9534532 0 -5.3901317 -0.27750815 + 300 1.0583027 -6.8483105 0 -5.2609672 -0.30347708 + 400 1.0493719 -6.8648608 0 -5.2909127 -0.15312495 + 500 1.0723786 -6.8341085 0 -5.2256528 0.017227511 + 600 1.0545695 -6.8152957 0 -5.2335517 -0.024362439 + 700 1.0507193 -6.8076033 0 -5.2316344 -0.07101536 + 800 1.0531856 -6.9378568 0 -5.3581886 -0.053943939 + 900 1.0442995 -6.8501126 0 -5.2837726 -0.13347942 + 1000 1.0335049 -6.8883554 0 -5.3382062 -0.18420426 + 1100 1.0287276 -6.8298226 0 -5.2868389 -0.12081558 + 1200 1.0322527 -6.9462828 0 -5.3980117 -0.18047625 + 1300 1.0599443 -6.9449975 0 -5.355192 -0.011763589 + 1400 1.0560932 -6.845479 0 -5.2614498 0.032130055 + 1500 1.0432786 -6.9035877 0 -5.338779 -0.10268662 + 1600 1.064183 -6.9116836 0 -5.3155205 -0.060722129 + 1700 1.0586249 -6.8768278 0 -5.2890013 0.037005566 + 1800 1.0576064 -7.0060193 0 -5.4197204 -0.036211254 + 1900 1.0595141 -6.838741 0 -5.2495807 -0.12395681 + 2000 1.0650509 -6.897976 0 -5.3005111 0.003594807 + 2100 1.0768273 -6.8874245 0 -5.2722962 0.033283489 + 2200 1.0511606 -6.9823162 0 -5.4056854 0.015008427 + 2300 1.0461138 -6.8820601 0 -5.3129988 0.064646933 + 2400 1.0485369 -6.9437148 0 -5.3710191 -0.16534939 + 2500 1.0507221 -6.9394786 0 -5.3635054 -0.098289859 + 2600 1.0518352 -6.8947578 0 -5.3171152 -0.011666785 + 2700 1.0402369 -6.9273377 0 -5.3670913 0.035267073 + 2800 1.0426109 -6.912024 0 -5.3482168 0.049597305 + 2900 1.0358928 -6.9574778 0 -5.4037471 -0.063216561 + 3000 1.0351023 -6.9844192 0 -5.4318742 -0.10323465 + 3100 1.0255005 -6.9382486 0 -5.4001052 -0.073954735 + 3200 1.0150616 -6.9843183 0 -5.4618321 -0.095136405 + 3300 1.0118112 -6.9522082 0 -5.4345973 -0.12686179 + 3400 1.0071522 -6.970158 0 -5.4595351 -0.012487475 + 3500 1.0041758 -6.9773019 0 -5.4711433 -0.098027653 + 3600 1.0189298 -6.9393039 0 -5.4110158 0.061631719 + 3700 1.012442 -6.9341423 0 -5.4155852 0.10442772 + 3800 1.0021246 -6.9594374 0 -5.4563553 -0.081535223 + 3900 1.0165002 -6.9045321 0 -5.3798882 -0.0088283303 + 4000 1.0077099 -6.9145511 0 -5.4030918 0.048349691 +Loop time of 135.409 on 1 procs for 4000 steps with 14333 atoms + +Performance: 25522.736 tau/day, 29.540 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 93.074 | 93.074 | 93.074 | 0.0 | 68.74 +Neigh | 40.192 | 40.192 | 40.192 | 0.0 | 29.68 +Comm | 0.19625 | 0.19625 | 0.19625 | 0.0 | 0.14 +Output | 0.41756 | 0.41756 | 0.41756 | 0.0 | 0.31 +Modify | 1.0706 | 1.0706 | 1.0706 | 0.0 | 0.79 +Other | | 0.4581 | | | 0.34 + +Nlocal: 14333 ave 14333 max 14333 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11 ave 11 max 11 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 401803 ave 401803 max 401803 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 803606 ave 803606 max 803606 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 803606 +Ave neighs/atom = 56.0668 +Neighbor list builds = 1050 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:02:15 diff --git a/examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.4 b/examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.4 new file mode 100644 index 0000000000..ec3d8fbddc --- /dev/null +++ b/examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.4 @@ -0,0 +1,147 @@ +LAMMPS (11 Aug 2017) +######################################################################## +#### 3D droplet oscilation using many-body DPD simulation ### +#### ### +#### Created : Zhen Li (zhen_li@brown.edu) ### +#### Division of Applied Mathematics, Brown University. ### +#### ### +#### mDPD parameters follow the choice of the publication: ### +#### Z. Li et al. "Three dimensional flow structures in a moving ### +#### droplet on substrate: a dissipative particle dynamics study" ### +#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.3 bin +neigh_modify every 1 delay 0 check yes + +atom_style mdpd + +region mdpd block -25 25 -10 10 -10 10 units box +create_box 1 mdpd +Created orthogonal box = (-25 -10 -10) to (25 10 10) + 4 by 1 by 1 MPI processor grid + +lattice fcc 6 +Lattice spacing in x,y,z = 0.87358 0.87358 0.87358 +region film block -20 20 -7.5 7.5 -2.0 2.0 units box +create_atoms 1 region film +Created 14333 atoms + +pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598 +pair_coeff 1 1 mdpd/rhosum 0.75 +pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75 +mass 1 1.0 + +compute mythermo all temp +thermo 100 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 38497 loop local dist gaussian + +fix mvv all mvv/dpd + +dump mydump all atom 100 atom.lammpstrj + +#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 # view 90 90 box no 0 size 600 200 +#dump_modify jpg pad 4 + +#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 # view 90 90 box no 0 size 600 200 +#dump_modify avi pad 4 + +timestep 0.01 +run 4000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 77 31 31 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair mdpd/rhosum, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair mdpd, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 6.265 | 6.655 | 7.045 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1 -13.346542 0 -11.846647 -6.9757225 + 100 1.0406108 -7.2500697 0 -5.6892624 -0.80306477 + 200 1.0535506 -6.9452928 0 -5.3650772 -0.39911584 + 300 1.0644295 -6.8599907 0 -5.2634577 -0.2997968 + 400 1.0780123 -6.9471342 0 -5.3302286 -0.06274869 + 500 1.0672153 -6.8269984 0 -5.2262872 0.021251762 + 600 1.0634304 -6.8366569 0 -5.2416226 -0.021863333 + 700 1.0544807 -6.8272074 0 -5.2455967 -0.0064688066 + 800 1.0556172 -6.8859788 0 -5.3026634 0.023983333 + 900 1.0436201 -6.9246523 0 -5.3593313 -0.12409618 + 1000 1.0617016 -6.8632331 0 -5.2707919 -0.1145505 + 1100 1.0323831 -6.951554 0 -5.4030874 -0.030031884 + 1200 1.0407785 -6.931048 0 -5.3699892 -0.018362136 + 1300 1.0380953 -6.8785296 0 -5.3214953 -0.099308737 + 1400 1.0418898 -6.8998 0 -5.3370743 -0.14199421 + 1500 1.0487254 -6.9671212 0 -5.3941429 -0.12132644 + 1600 1.0561042 -6.8948881 0 -5.3108424 -0.09627292 + 1700 1.0524479 -6.9531441 0 -5.3745823 -0.11959782 + 1800 1.0541197 -6.9219819 0 -5.3409126 0.032964029 + 1900 1.0531221 -6.8805815 0 -5.3010085 0.030124685 + 2000 1.0531819 -6.8612868 0 -5.2816242 -0.076876781 + 2100 1.0757791 -6.919875 0 -5.3063189 -0.04060439 + 2200 1.069423 -6.9005754 0 -5.2965527 0.015347467 + 2300 1.0403109 -6.9015402 0 -5.3411827 0.0034687897 + 2400 1.0547448 -6.9325539 0 -5.3505471 -0.021202325 + 2500 1.0404195 -6.8494675 0 -5.2889472 0.086947847 + 2600 1.0499828 -6.9861392 0 -5.4112749 -0.018079308 + 2700 1.0294278 -6.8525151 0 -5.3084811 0.16911472 + 2800 1.0220652 -6.8993978 0 -5.366407 0.064820531 + 2900 1.0347904 -6.9322703 0 -5.3801929 -0.11384964 + 3000 1.0391372 -6.9519088 0 -5.3933117 0.003050577 + 3100 1.0335828 -7.0090074 0 -5.4587413 -0.17366664 + 3200 1.0211896 -6.9421289 0 -5.4104513 0.025299853 + 3300 1.0019232 -6.9426488 0 -5.4398688 -0.098334724 + 3400 1.0203541 -6.9310981 0 -5.4006737 -0.0015544982 + 3500 1.0076794 -6.9519932 0 -5.4405796 -0.056956902 + 3600 1.0086525 -6.9620979 0 -5.4492247 0.020014884 + 3700 1.0046112 -7.0011625 0 -5.4943508 -0.083936527 + 3800 1.0096867 -6.9470382 0 -5.4326138 -0.089521759 + 3900 1.0074482 -6.9959414 0 -5.4848745 -0.11873698 + 4000 1.01222 -6.9535694 0 -5.4353454 0.042191466 +Loop time of 63.0327 on 4 procs for 4000 steps with 14333 atoms + +Performance: 54828.695 tau/day, 63.459 timesteps/s +98.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 16.591 | 29.795 | 42.814 | 236.6 | 47.27 +Neigh | 2.0347 | 10.239 | 18.555 | 255.6 | 16.24 +Comm | 0.70099 | 6.0601 | 11.386 | 207.4 | 9.61 +Output | 0.20713 | 0.40902 | 0.61087 | 31.5 | 0.65 +Modify | 0.058089 | 0.27033 | 0.4851 | 40.7 | 0.43 +Other | | 16.26 | | | 25.79 + +Nlocal: 3583.25 ave 7207 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1055.75 ave 2131 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 100549 ave 202192 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 201098 ave 404372 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 804390 +Ave neighs/atom = 56.1215 +Neighbor list builds = 1049 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:03 diff --git a/examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.1 b/examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.1 new file mode 100644 index 0000000000..a872600504 --- /dev/null +++ b/examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.1 @@ -0,0 +1,24 @@ +# Chunk-averaged data for fix stat and group c_cc2 +# Timestep Number-of-chunks Total-count +# Chunk Coord1 Ncount c_cc1 c_cc2 +100 20 16000 + 1 -9.5 797.17 0.986661 1.0077 + 2 -8.5 802.61 0.967974 1.02003 + 3 -7.5 795.46 0.957045 1.02873 + 4 -6.5 806.46 0.951271 1.03428 + 5 -5.5 802.34 0.94898 1.03692 + 6 -4.5 799.84 0.949378 1.03673 + 7 -3.5 798.4 0.952505 1.03374 + 8 -2.5 800.36 0.959322 1.02778 + 9 -1.5 797.65 0.971516 1.01867 + 10 -0.5 808.88 0.990644 1.00626 + 11 0.5 786.29 1.00924 0.993828 + 12 1.5 807.16 1.02831 0.981436 + 13 2.5 797.54 1.04071 0.972184 + 14 3.5 799.67 1.04749 0.966258 + 15 4.5 799.61 1.05063 0.963256 + 16 5.5 806.11 1.05105 0.963052 + 17 6.5 803.67 1.04877 0.965688 + 18 7.5 797.39 1.04305 0.971187 + 19 8.5 801.85 1.03208 0.97993 + 20 9.5 791.54 1.01351 0.992209 diff --git a/examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.4 b/examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.4 new file mode 100644 index 0000000000..de34ef26c3 --- /dev/null +++ b/examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.4 @@ -0,0 +1,24 @@ +# Chunk-averaged data for fix stat and group c_cc2 +# Timestep Number-of-chunks Total-count +# Chunk Coord1 Ncount c_cc1 c_cc2 +100 20 16000 + 1 -9.5 806.92 0.986675 1.00766 + 2 -8.5 798.01 0.96792 1.02003 + 3 -7.5 805.43 0.956909 1.02883 + 4 -6.5 800.54 0.951207 1.03432 + 5 -5.5 794.14 0.948967 1.03691 + 6 -4.5 799.75 0.949379 1.03672 + 7 -3.5 799.65 0.952492 1.03374 + 8 -2.5 799.94 0.959331 1.02778 + 9 -1.5 800.96 0.971664 1.01861 + 10 -0.5 803.97 0.99074 1.00622 + 11 0.5 800.66 1.00949 0.993673 + 12 1.5 779.22 1.02824 0.981461 + 13 2.5 809.13 1.04056 0.972274 + 14 3.5 805.23 1.04747 0.966272 + 15 4.5 795.95 1.05061 0.96327 + 16 5.5 796.4 1.05105 0.963035 + 17 6.5 806.1 1.04883 0.965621 + 18 7.5 806.41 1.04305 0.971224 + 19 8.5 792.2 1.03211 0.979955 + 20 9.5 799.39 1.01362 0.992156 diff --git a/examples/USER/meso/tdpd/in.tdpd b/examples/USER/meso/tdpd/in.tdpd new file mode 100644 index 0000000000..748a4f5077 --- /dev/null +++ b/examples/USER/meso/tdpd/in.tdpd @@ -0,0 +1,54 @@ +######################################################################## +### Pure diffusion with a reaction source term analog of a periodic ### +### Poiseuille flow problem using transport DPD (tDPD) simulation ### +### ### +### Created : Zhen Li (zhen_li@brown.edu) ### +### Division of Applied Mathematics, Brown University. ### +### ### +### tDPD system setup follows Fig.1 in the publication: ### +### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ### +### "Transport dissipative particle dynamics model for mesoscopic ### +### advection-diffusion-reaction problems. J. Chem. Phys., ### +### 2015, 143: 014101. DOI: 10.1063/1.4923254 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes + +atom_style tdpd 2 + +region tdpd block -10 10 -10 10 -5 5 units box +create_box 1 tdpd +create_atoms 1 random 16000 276438 NULL +mass 1 1.0 +set atom * cc 1 1.0 +set atom * cc 2 1.0 + +pair_style tdpd 1.0 1.58 9872598 +pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 + +compute mythermo all temp +thermo 50 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 432982 loop local dist gaussian + +fix mvv all mvv/tdpd 0.5 +fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 +fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 +fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01 +fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01 + +timestep 0.01 +run 500 +reset_timestep 0 + +compute cc1 all tdpd/cc/atom 1 +compute cc2 all tdpd/cc/atom 2 +compute bin all chunk/atom bin/1d y 0.0 1.0 +fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile + +run 100 diff --git a/examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.1 b/examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.1 new file mode 100644 index 0000000000..21b618148c --- /dev/null +++ b/examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.1 @@ -0,0 +1,146 @@ +LAMMPS (11 Aug 2017) +######################################################################## +### Pure diffusion with a reaction source term analog of a periodic ### +### Poiseuille flow problem using transport DPD (tDPD) simulation ### +### ### +### Created : Zhen Li (zhen_li@brown.edu) ### +### Division of Applied Mathematics, Brown University. ### +### ### +### tDPD system setup follows Fig.1 in the publication: ### +### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ### +### "Transport dissipative particle dynamics model for mesoscopic ### +### advection-diffusion-reaction problems. J. Chem. Phys., ### +### 2015, 143: 014101. DOI: 10.1063/1.4923254 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes + +atom_style tdpd 2 + +region tdpd block -10 10 -10 10 -5 5 units box +create_box 1 tdpd +Created orthogonal box = (-10 -10 -5) to (10 10 5) + 1 by 1 by 1 MPI processor grid +create_atoms 1 random 16000 276438 NULL +Created 16000 atoms +mass 1 1.0 +set atom * cc 1 1.0 + 16000 settings made for cc index 1 +set atom * cc 2 1.0 + 16000 settings made for cc index 2 + +pair_style tdpd 1.0 1.58 9872598 +pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 + +compute mythermo all temp +thermo 50 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 432982 loop local dist gaussian + +fix mvv all mvv/tdpd 0.5 +fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 +fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 +fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01 +fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01 + +timestep 0.01 +run 500 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.78 + ghost atom cutoff = 1.78 + binsize = 0.89, bins = 23 23 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair tdpd, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.3 | 11.3 | 11.3 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1 48.948932 0 50.448838 202.19166 + 50 0.99837766 43.949877 0 45.447349 195.80936 + 100 0.99846831 43.756995 0 45.254604 198.22348 + 150 1.0026903 43.72408 0 45.228021 196.61676 + 200 1.0063144 43.722388 0 45.231765 194.17954 + 250 1.0032304 43.721864 0 45.226615 197.85829 + 300 0.9932656 43.703526 0 45.193331 196.57406 + 350 1.0002916 43.720498 0 45.220841 193.55346 + 400 0.99475486 43.722965 0 45.215004 196.81546 + 450 1.0011803 43.712447 0 45.214124 200.46118 + 500 1.0009006 43.708984 0 45.210241 197.38953 +Loop time of 96.0326 on 1 procs for 500 steps with 16000 atoms + +Performance: 4498.474 tau/day, 5.207 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 90.083 | 90.083 | 90.083 | 0.0 | 93.80 +Neigh | 5.049 | 5.049 | 5.049 | 0.0 | 5.26 +Comm | 0.34141 | 0.34141 | 0.34141 | 0.0 | 0.36 +Output | 0.00092816 | 0.00092816 | 0.00092816 | 0.0 | 0.00 +Modify | 0.45991 | 0.45991 | 0.45991 | 0.0 | 0.48 +Other | | 0.09865 | | | 0.10 + +Nlocal: 16000 ave 16000 max 16000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 14091 ave 14091 max 14091 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 749379 ave 749379 max 749379 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 749379 +Ave neighs/atom = 46.8362 +Neighbor list builds = 183 +Dangerous builds = 0 +reset_timestep 0 + +compute cc1 all tdpd/cc/atom 1 +compute cc2 all tdpd/cc/atom 2 +compute bin all chunk/atom bin/1d y 0.0 1.0 +fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile + +run 100 +Per MPI rank memory allocation (min/avg/max) = 11.8 | 11.8 | 11.8 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.0009006 43.708984 0 45.210241 199.3205 + 50 1.0007276 43.704844 0 45.205842 197.77053 + 100 1.0039032 43.714201 0 45.219961 197.31118 +Loop time of 19.0326 on 1 procs for 100 steps with 16000 atoms + +Performance: 4539.577 tau/day, 5.254 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 17.842 | 17.842 | 17.842 | 0.0 | 93.74 +Neigh | 0.98674 | 0.98674 | 0.98674 | 0.0 | 5.18 +Comm | 0.066013 | 0.066013 | 0.066013 | 0.0 | 0.35 +Output | 0.00016284 | 0.00016284 | 0.00016284 | 0.0 | 0.00 +Modify | 0.11795 | 0.11795 | 0.11795 | 0.0 | 0.62 +Other | | 0.02012 | | | 0.11 + +Nlocal: 16000 ave 16000 max 16000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 14126 ave 14126 max 14126 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 748927 ave 748927 max 748927 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 748927 +Ave neighs/atom = 46.8079 +Neighbor list builds = 37 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:55 diff --git a/examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.4 b/examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.4 new file mode 100644 index 0000000000..6cd99168f4 --- /dev/null +++ b/examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.4 @@ -0,0 +1,146 @@ +LAMMPS (11 Aug 2017) +######################################################################## +### Pure diffusion with a reaction source term analog of a periodic ### +### Poiseuille flow problem using transport DPD (tDPD) simulation ### +### ### +### Created : Zhen Li (zhen_li@brown.edu) ### +### Division of Applied Mathematics, Brown University. ### +### ### +### tDPD system setup follows Fig.1 in the publication: ### +### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ### +### "Transport dissipative particle dynamics model for mesoscopic ### +### advection-diffusion-reaction problems. J. Chem. Phys., ### +### 2015, 143: 014101. DOI: 10.1063/1.4923254 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes + +atom_style tdpd 2 + +region tdpd block -10 10 -10 10 -5 5 units box +create_box 1 tdpd +Created orthogonal box = (-10 -10 -5) to (10 10 5) + 2 by 2 by 1 MPI processor grid +create_atoms 1 random 16000 276438 NULL +Created 16000 atoms +mass 1 1.0 +set atom * cc 1 1.0 + 16000 settings made for cc index 1 +set atom * cc 2 1.0 + 16000 settings made for cc index 2 + +pair_style tdpd 1.0 1.58 9872598 +pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 + +compute mythermo all temp +thermo 50 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 432982 loop local dist gaussian + +fix mvv all mvv/tdpd 0.5 +fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 +fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 +fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01 +fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01 + +timestep 0.01 +run 500 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.78 + ghost atom cutoff = 1.78 + binsize = 0.89, bins = 23 23 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair tdpd, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.814 | 4.823 | 4.829 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1 48.948932 0 50.448838 199.65978 + 50 1.0153476 43.948796 0 45.471722 198.3346 + 100 1.0064284 43.754875 0 45.264424 197.5308 + 150 0.99609985 43.726751 0 45.220807 197.50623 + 200 1.0016604 43.720283 0 45.22268 197.81129 + 250 1.0054979 43.718568 0 45.22672 195.79405 + 300 0.9997618 43.716617 0 45.216166 197.84788 + 350 0.99170101 43.72093 0 45.208389 196.07711 + 400 1.0043692 43.71648 0 45.22294 199.55247 + 450 1.0086263 43.709988 0 45.222833 198.20516 + 500 1.0029076 43.717879 0 45.222146 197.26281 +Loop time of 24.5533 on 4 procs for 500 steps with 16000 atoms + +Performance: 17594.412 tau/day, 20.364 timesteps/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 22.236 | 22.418 | 22.736 | 4.0 | 91.30 +Neigh | 1.2759 | 1.2883 | 1.3077 | 1.1 | 5.25 +Comm | 0.35749 | 0.69526 | 0.88462 | 24.1 | 2.83 +Output | 0.00043321 | 0.00050318 | 0.00070691 | 0.0 | 0.00 +Modify | 0.11555 | 0.11648 | 0.11888 | 0.4 | 0.47 +Other | | 0.03473 | | | 0.14 + +Nlocal: 4000 ave 4012 max 3982 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 5986.25 ave 6016 max 5956 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Neighs: 187309 ave 188264 max 186087 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 749235 +Ave neighs/atom = 46.8272 +Neighbor list builds = 180 +Dangerous builds = 0 +reset_timestep 0 + +compute cc1 all tdpd/cc/atom 1 +compute cc2 all tdpd/cc/atom 2 +compute bin all chunk/atom bin/1d y 0.0 1.0 +fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile + +run 100 +Per MPI rank memory allocation (min/avg/max) = 5.065 | 5.074 | 5.082 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.0029076 43.717879 0 45.222146 198.45789 + 50 1.0077982 43.713264 0 45.224867 196.56183 + 100 1.0036823 43.708022 0 45.213451 196.00815 +Loop time of 4.79577 on 4 procs for 100 steps with 16000 atoms + +Performance: 18015.870 tau/day, 20.852 timesteps/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.3481 | 4.39 | 4.4398 | 1.7 | 91.54 +Neigh | 0.25477 | 0.25675 | 0.25963 | 0.4 | 5.35 +Comm | 0.059327 | 0.11194 | 0.15608 | 11.0 | 2.33 +Output | 0.00011206 | 0.00011748 | 0.00011992 | 0.0 | 0.00 +Modify | 0.030417 | 0.030622 | 0.030739 | 0.1 | 0.64 +Other | | 0.006301 | | | 0.13 + +Nlocal: 4000 ave 4010 max 3987 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Nghost: 5985.25 ave 6025 max 5959 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Neighs: 187304 ave 188092 max 186449 min +Histogram: 1 0 0 0 0 2 0 0 0 1 + +Total # of neighbors = 749216 +Ave neighs/atom = 46.826 +Neighbor list builds = 38 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:29 diff --git a/src/Makefile b/src/Makefile index 3b67d2284f..91d65a11c5 100644 --- a/src/Makefile +++ b/src/Makefile @@ -59,7 +59,8 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ PACKUSER = user-atc user-awpmd user-cgdna user-cgsdk user-colvars \ user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ - user-intel user-lb user-manifold user-meamc user-mgpt user-misc user-molfile \ + user-intel user-lb user-manifold user-meamc user-meso \ + user-mgpt user-misc user-molfile \ user-netcdf user-omp user-phonon user-qmmm user-qtb \ user-quip user-reaxc user-smd user-smtbq user-sph user-tally \ user-vtk diff --git a/src/USER-MESO/README b/src/USER-MESO/README new file mode 100644 index 0000000000..0119fdb9f8 --- /dev/null +++ b/src/USER-MESO/README @@ -0,0 +1,50 @@ +This package implements three extensions of the dissipative particle +dynamics (DPD) method, i.e., energy-conserving DPD (eDPD) that can +model non-isothermal processes, many-body DPD (mDPD) for simulating +vapor-liquid coexistence, and transport DPD (tDPD) for modeling +advection-diffuion-reaction systems. The equations of motion of these +DPD extensions are integrated through the modified velocity-Verlet +(MVV) algorithm. + +Currently, the package has the following features: + +* Three new atom styles (eDPD, mDPD, tDPD) for tracking the particles + with internal temperature, local mass density, and chemical + concentration. + +* Three set commands (edpd/temp, edpd/cv, cc) for setting internal + temperature (edpd/temp) and heat capacity (edpd/cv) for eDPD + particles and for setting chemical concentration (cc) for tDPD + particles. + +* Two compute commands (edpd/temp/atom, tdpd/cc/atom) for accessing + the internal temperature of eDPD particles and the chemical + concentration of tDPD particles. + +* Three fix commands (mvv/dpd, mvv/edpd, mvv/tdpd) for integrating the + shochastic ODEs using the modified velocity-Verlet (MVV) algorithm. + +* Two fix commands (edpd/source, tdpd/source) for adding additional + heat source/sink or chemical concentration source/sink to eDPD and + tDPD particles. + +* One pair style (edpd) for modeling a eDPD fluid. + +* Two pair styles (mdpd/rhosum, mdpd) for modeling a mDPD fluid. + +* One pair style (tdpd) for modeling a tDPD fluid. + +See the doc pages for "atom style edpd", "atom style mdpd", "atom +style tdpd", "set edpd/temp", "set edpd/cv", "set tdpd/cc", "compute +edpd/temp/atom", "compute tdpd/cc/atom", "fix mvv/dpd", "fix +mvv/edpd", "fix mvv/tdpd", "fix edpd/source", "fix tdpd/source", "pair +edpd", "pair mdpd/rhosum", "pair mdpd", "pair tdpd" commands to get +started. At the bottom of the doc pages are many links to additional +documentation contained in the doc/USER/meso directory. + +There are example scripts for using this package in +examples/USER/meso. + +The person who created this package is Zhen Li (zhen_li at brown.edu) +at Division of Applied Mathematics, Brown University, USA. Contact him +directly if you have questions. diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESO/atom_vec_edpd.cpp new file mode 100644 index 0000000000..635743cc9e --- /dev/null +++ b/src/USER-MESO/atom_vec_edpd.cpp @@ -0,0 +1,844 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +#include +#include +#include "atom_vec_edpd.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "modify.h" +#include "fix.h" +#include "update.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +AtomVecEDPD::AtomVecEDPD(LAMMPS *lmp) : AtomVec(lmp) +{ + if(strcmp(update->unit_style,"lj") != 0) + error->all(FLERR,"Atom style edpd requires lj units"); + + molecular = 0; + mass_type = 1; + forceclearflag = 1; + + comm_x_only = comm_f_only = 0; + comm->ghost_velocity = 1; + + size_forward = 3 + 5; // edpd_temp + vest[4] + size_reverse = 3 + 1; // edpd_flux + size_border = 6 + 6; // edpd_temp + edpd_cv + vest[4] + size_velocity = 3; + size_data_atom = 5 + 2; // we read id + type + edpd_temp + edpd_cv + xyz[3] + size_data_vel = 4; + xcol_data = 5; + + atom->edpd_flag = 1; + atom->vest_flag = 1; +} + +/* ---------------------------------------------------------------------- + grow atom arrays + n = 0 grows arrays by a chunk + n > 0 allocates arrays to size n +------------------------------------------------------------------------- */ + +void AtomVecEDPD::grow(int n) +{ + if (n == 0) grow_nmax(); + else nmax = n; + atom->nmax = nmax; + if (nmax < 0 || nmax > MAXSMALLINT) + error->one(FLERR,"Per-processor system is too big"); + + tag = memory->grow(atom->tag,nmax,"atom:tag"); + type = memory->grow(atom->type,nmax,"atom:type"); + mask = memory->grow(atom->mask,nmax,"atom:mask"); + image = memory->grow(atom->image,nmax,"atom:image"); + x = memory->grow(atom->x,nmax,3,"atom:x"); + v = memory->grow(atom->v,nmax,3,"atom:v"); + f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f"); + edpd_cv= memory->grow(atom->edpd_cv, nmax, "atom:edpd_cv"); + edpd_temp = memory->grow(atom->edpd_temp, nmax, "atom:edpd_temp"); + edpd_flux = memory->grow(atom->edpd_flux, nmax*comm->nthreads,"atom:edpd_flux"); + vest = memory->grow(atom->vest, nmax, 4, "atom:vest"); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax); +} + +/* ---------------------------------------------------------------------- + reset local array ptrs +------------------------------------------------------------------------- */ + +void AtomVecEDPD::grow_reset() +{ + tag = atom->tag; type = atom->type; + mask = atom->mask; image = atom->image; + x = atom->x; v = atom->v; f = atom->f; + edpd_cv = atom->cv; edpd_temp = atom->edpd_temp; edpd_flux = atom->edpd_flux; + vest = atom->vest; +} + +/* ---------------------------------------------------------------------- + copy atom I info to atom J +------------------------------------------------------------------------- */ + +void AtomVecEDPD::copy(int i, int j, int delflag) +{ + tag[j] = tag[i]; + type[j] = type[i]; + mask[j] = mask[i]; + image[j] = image[i]; + x[j][0] = x[i][0]; + x[j][1] = x[i][1]; + x[j][2] = x[i][2]; + v[j][0] = v[i][0]; + v[j][1] = v[i][1]; + v[j][2] = v[i][2]; + + edpd_temp[j] = edpd_temp[i]; + edpd_flux[j] = edpd_flux[i]; + edpd_cv[j] = edpd_cv[i]; + vest[j][0] = vest[i][0]; + vest[j][1] = vest[i][1]; + vest[j][2] = vest[i][2]; + vest[j][3] = vest[i][3]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); +} + + +void AtomVecEDPD::force_clear(int n, size_t nbytes) +{ + memset(&edpd_flux[n],0,nbytes); +} + + +/* ---------------------------------------------------------------------- */ + +int AtomVecEDPD::pack_comm(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,k,m; + double dx,dy,dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = edpd_temp[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + buf[m++] = vest[j][3]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; + dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; + dz = pbc[2]*domain->zprd; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = edpd_temp[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + buf[m++] = vest[j][3]; + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecEDPD::pack_comm_vel(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,k,m; + double dx,dy,dz,dvx,dvy,dvz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + buf[m++] = edpd_temp[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + buf[m++] = vest[j][3]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; + dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; + dz = pbc[2]*domain->zprd; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + buf[m++] = edpd_temp[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + buf[m++] = vest[j][3]; + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + if (mask[i] & deform_groupbit) { + buf[m++] = v[j][0] + dvx; + buf[m++] = v[j][1] + dvy; + buf[m++] = v[j][2] + dvz; + } else { + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + buf[m++] = edpd_temp[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + buf[m++] = vest[j][3]; + } + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecEDPD::unpack_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + edpd_temp[i] = buf[m++]; + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + vest[i][3] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecEDPD::unpack_comm_vel(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + v[i][0] = buf[m++]; + v[i][1] = buf[m++]; + v[i][2] = buf[m++]; + edpd_temp[i] = buf[m++]; + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + vest[i][3] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecEDPD::pack_reverse(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + buf[m++] = f[i][0]; + buf[m++] = f[i][1]; + buf[m++] = f[i][2]; + buf[m++] = edpd_flux[i]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecEDPD::unpack_reverse(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + f[j][0] += buf[m++]; + f[j][1] += buf[m++]; + f[j][2] += buf[m++]; + edpd_flux[j] += buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecEDPD::pack_border(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = edpd_temp[j]; + buf[m++] = edpd_cv[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + buf[m++] = vest[j][3]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = edpd_temp[j]; + buf[m++] = edpd_cv[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + buf[m++] = vest[j][3]; + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecEDPD::pack_border_vel(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz,dvx,dvy,dvz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = edpd_temp[j]; + buf[m++] = edpd_cv[j]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + buf[m++] = vest[j][3]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = edpd_temp[j]; + buf[m++] = edpd_cv[j]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + buf[m++] = vest[j][3]; + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = edpd_temp[j]; + buf[m++] = edpd_cv[j]; + if (mask[i] & deform_groupbit) { + buf[m++] = v[j][0] + dvx; + buf[m++] = v[j][1] + dvy; + buf[m++] = v[j][2] + dvz; + buf[m++] = vest[j][0] + dvx; + buf[m++] = vest[j][1] + dvy; + buf[m++] = vest[j][2] + dvz; + buf[m++] = vest[j][3]; + } else { + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + buf[m++] = vest[j][3]; + } + } + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecEDPD::unpack_border(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) grow(0); + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + tag[i] = (tagint) ubuf(buf[m++]).i; + type[i] = (int) ubuf(buf[m++]).i; + mask[i] = (int) ubuf(buf[m++]).i; + edpd_temp[i] = buf[m++]; + edpd_cv[i] = buf[m++]; + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + vest[i][3] = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecEDPD::unpack_border_vel(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) grow(0); + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + tag[i] = (tagint) ubuf(buf[m++]).i; + type[i] = (int) ubuf(buf[m++]).i; + mask[i] = (int) ubuf(buf[m++]).i; + edpd_temp[i] = buf[m++]; + edpd_cv[i] = buf[m++]; + v[i][0] = buf[m++]; + v[i][1] = buf[m++]; + v[i][2] = buf[m++]; + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + vest[i][3] = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); +} + +/* ---------------------------------------------------------------------- + pack data for atom I for sending to another proc + xyz must be 1st 3 values, so comm::exchange() can test on them +------------------------------------------------------------------------- */ + +int AtomVecEDPD::pack_exchange(int i, double *buf) +{ + int m = 1; + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + buf[m++] = v[i][0]; + buf[m++] = v[i][1]; + buf[m++] = v[i][2]; + buf[m++] = ubuf(tag[i]).d; + buf[m++] = ubuf(type[i]).d; + buf[m++] = ubuf(mask[i]).d; + buf[m++] = ubuf(image[i]).d; + buf[m++] = edpd_temp[i]; + buf[m++] = edpd_cv[i]; + buf[m++] = vest[i][0]; + buf[m++] = vest[i][1]; + buf[m++] = vest[i][2]; + buf[m++] = vest[i][3]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecEDPD::unpack_exchange(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + int m = 1; + x[nlocal][0] = buf[m++]; + x[nlocal][1] = buf[m++]; + x[nlocal][2] = buf[m++]; + v[nlocal][0] = buf[m++]; + v[nlocal][1] = buf[m++]; + v[nlocal][2] = buf[m++]; + tag[nlocal] = (tagint) ubuf(buf[m++]).i; + type[nlocal] = (int) ubuf(buf[m++]).i; + mask[nlocal] = (int) ubuf(buf[m++]).i; + image[nlocal] = (imageint) ubuf(buf[m++]).i; + edpd_temp[nlocal] = buf[m++]; + edpd_cv[nlocal] = buf[m++]; + vest[nlocal][0] = buf[m++]; + vest[nlocal][1] = buf[m++]; + vest[nlocal][2] = buf[m++]; + vest[nlocal][3] = buf[m++]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]-> + unpack_exchange(nlocal,&buf[m]); + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + size of restart data for all atoms owned by this proc + include extra data stored by fixes +------------------------------------------------------------------------- */ + +int AtomVecEDPD::size_restart() +{ + int i; + + int nlocal = atom->nlocal; + int n = (11 + 6) * nlocal; // 11 + edpd_temp + edpd_cv + vest[4] + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + for (i = 0; i < nlocal; i++) + n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); + + return n; +} + +/* ---------------------------------------------------------------------- + pack atom I's data for restart file including extra quantities + xyz must be 1st 3 values, so that read_restart can test on them + molecular types may be negative, but write as positive +------------------------------------------------------------------------- */ + +int AtomVecEDPD::pack_restart(int i, double *buf) +{ + int m = 1; + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + buf[m++] = ubuf(tag[i]).d; + buf[m++] = ubuf(type[i]).d; + buf[m++] = ubuf(mask[i]).d; + buf[m++] = ubuf(image[i]).d; + buf[m++] = v[i][0]; + buf[m++] = v[i][1]; + buf[m++] = v[i][2]; + buf[m++] = edpd_temp[i]; + buf[m++] = edpd_cv[i]; + buf[m++] = vest[i][0]; + buf[m++] = vest[i][1]; + buf[m++] = vest[i][2]; + buf[m++] = vest[i][3]; + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- + unpack data for one atom from restart file including extra quantities +------------------------------------------------------------------------- */ + +int AtomVecEDPD::unpack_restart(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) { + grow(0); + if (atom->nextra_store) + memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); + } + + int m = 1; + x[nlocal][0] = buf[m++]; + x[nlocal][1] = buf[m++]; + x[nlocal][2] = buf[m++]; + tag[nlocal] = (tagint) ubuf(buf[m++]).i; + type[nlocal] = (int) ubuf(buf[m++]).i; + mask[nlocal] = (int) ubuf(buf[m++]).i; + image[nlocal] = (imageint) ubuf(buf[m++]).i; + v[nlocal][0] = buf[m++]; + v[nlocal][1] = buf[m++]; + v[nlocal][2] = buf[m++]; + + edpd_temp[nlocal] = buf[m++]; + edpd_cv[nlocal]= buf[m++]; + vest[nlocal][0] = buf[m++]; + vest[nlocal][1] = buf[m++]; + vest[nlocal][2] = buf[m++]; + vest[nlocal][3] = buf[m++]; + + double **extra = atom->extra; + if (atom->nextra_store) { + int size = static_cast (buf[0]) - m; + for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; + } + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + create one atom of itype at coord + set other values to defaults +------------------------------------------------------------------------- */ + +void AtomVecEDPD::create_atom(int itype, double *coord) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + tag[nlocal] = 0; + type[nlocal] = itype; + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + mask[nlocal] = 1; + image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + + edpd_temp[nlocal] = 1.0; + edpd_flux[nlocal] = 0.0; + edpd_cv[nlocal]= 1.0E5; + vest[nlocal][0] = 0.0; + vest[nlocal][1] = 0.0; + vest[nlocal][2] = 0.0; + vest[nlocal][3] = edpd_temp[nlocal]; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack one line from Atoms section of data file + initialize other atom quantities +------------------------------------------------------------------------- */ + +void AtomVecEDPD::data_atom(double *coord, imageint imagetmp, char **values) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + tag[nlocal] = ATOTAGINT(values[0]); + type[nlocal] = atoi(values[1]); + if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) + error->one(FLERR,"Invalid atom type in Atoms section of data file"); + + edpd_temp[nlocal] = atof(values[2]); + edpd_cv[nlocal] = atof(values[3]); + + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + + image[nlocal] = imagetmp; + + mask[nlocal] = 1; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + + vest[nlocal][0] = 0.0; + vest[nlocal][1] = 0.0; + vest[nlocal][2] = 0.0; + vest[nlocal][3] = edpd_temp[nlocal]; + edpd_flux[nlocal] = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + pack atom info for data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecEDPD::pack_data(double **buf) +{ + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + buf[i][0] = ubuf(tag[i]).d; + buf[i][1] = ubuf(type[i]).d; + buf[i][2] = edpd_temp[i]; + buf[i][3] = edpd_cv[i]; + buf[i][4] = x[i][0]; + buf[i][5] = x[i][1]; + buf[i][6] = x[i][2]; + buf[i][7] = ubuf((image[i] & IMGMASK) - IMGMAX).d; + buf[i][8] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d; + buf[i][9] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d; + } +} + +/* ---------------------------------------------------------------------- + write atom info to data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecEDPD::write_data(FILE *fp, int n, double **buf) +{ + for (int i = 0; i < n; i++) + fprintf(fp,TAGINT_FORMAT " %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n", + (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i, + buf[i][2],buf[i][3],buf[i][4],buf[i][5],buf[i][6], + (int) ubuf(buf[i][7]).i,(int) ubuf(buf[i][8]).i,(int) ubuf(buf[i][9]).i); +} + +/* ---------------------------------------------------------------------- + return # of bytes of allocated memory +------------------------------------------------------------------------- */ + +bigint AtomVecEDPD::memory_usage() +{ + bigint bytes = 0; + + if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); + if (atom->memcheck("type")) bytes += memory->usage(type,nmax); + if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); + if (atom->memcheck("image")) bytes += memory->usage(image,nmax); + if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); + if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); + if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3); + if (atom->memcheck("edpd_temp")) bytes += memory->usage(edpd_temp,nmax); + if (atom->memcheck("edpd_flux")) bytes += memory->usage(edpd_flux,nmax*comm->nthreads); + if (atom->memcheck("edpd_cv")) bytes += memory->usage(edpd_cv,nmax); + if (atom->memcheck("vest")) bytes += memory->usage(vest,nmax,4); + + return bytes; +} diff --git a/src/USER-MESO/atom_vec_edpd.h b/src/USER-MESO/atom_vec_edpd.h new file mode 100644 index 0000000000..36a4cae97b --- /dev/null +++ b/src/USER-MESO/atom_vec_edpd.h @@ -0,0 +1,68 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef ATOM_CLASS + +AtomStyle(edpd,AtomVecEDPD) + +#else + +#ifndef LMP_ATOM_VEC_EDPD_H +#define LMP_ATOM_VEC_EDPD_H + +#include "atom_vec.h" + +namespace LAMMPS_NS { + +class AtomVecEDPD : public AtomVec { + public: + AtomVecEDPD(class LAMMPS *); + virtual ~AtomVecEDPD() {} + void grow(int); + void grow_reset(); + void copy(int, int, int); + void force_clear(int, size_t); + virtual int pack_comm(int, int *, double *, int, int *); + virtual int pack_comm_vel(int, int *, double *, int, int *); + virtual void unpack_comm(int, int, double *); + virtual void unpack_comm_vel(int, int, double *); + int pack_reverse(int, int, double *); + void unpack_reverse(int, int *, double *); + virtual int pack_border(int, int *, double *, int, int *); + virtual int pack_border_vel(int, int *, double *, int, int *); + virtual void unpack_border(int, int, double *); + virtual void unpack_border_vel(int, int, double *); + virtual int pack_exchange(int, double *); + virtual int unpack_exchange(double *); + int size_restart(); + int pack_restart(int, double *); + int unpack_restart(double *); + void create_atom(int, double *); + void data_atom(double *, imageint, char **); + void pack_data(double **); + void write_data(FILE *, int, double **); + bigint memory_usage(); + + protected: + tagint *tag; + int *type,*mask; + imageint *image; + double **x,**v,**f; + double **vest; // store intermediate velocity for using mvv integrator + double *edpd_temp,*edpd_flux,*edpd_cv; // temperature, heat flux, and heat capacity +}; + +} + +#endif +#endif diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESO/atom_vec_mdpd.cpp new file mode 100644 index 0000000000..0a4d302c36 --- /dev/null +++ b/src/USER-MESO/atom_vec_mdpd.cpp @@ -0,0 +1,951 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ------------------------------------------------------------------------- */ + +#include +#include +#include "atom_vec_mdpd.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "modify.h" +#include "fix.h" +#include "update.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +AtomVecMDPD::AtomVecMDPD(LAMMPS *lmp) : AtomVec(lmp) +{ + if(strcmp(update->unit_style,"lj") != 0) + error->all(FLERR,"Atom style mdpd requires lj units"); + + molecular = 0; + mass_type = 1; + forceclearflag = 1; + + comm_x_only = comm_f_only = 0; + comm->ghost_velocity = 1; + + size_forward = 3 + 4; // 3 + rho + vest[3], that means we may only communicate 4 in hybrid + size_reverse = 3 + 1; // 3 + drho + size_border = 6 + 4; // 6 + rho + vest[3] + size_velocity = 3; + size_data_atom = 5; + size_data_vel = 4; + xcol_data = 3; + + atom->rho_flag = 1; + atom->vest_flag = 1; +} + +/* ---------------------------------------------------------------------- + grow atom arrays + n = 0 grows arrays by a chunk + n > 0 allocates arrays to size n + ------------------------------------------------------------------------- */ + +void AtomVecMDPD::grow(int n) +{ + if (n == 0) grow_nmax(); + else nmax = n; + atom->nmax = nmax; + if (nmax < 0 || nmax > MAXSMALLINT) + error->one(FLERR,"Per-processor system is too big"); + + tag = memory->grow(atom->tag, nmax, "atom:tag"); + type = memory->grow(atom->type, nmax, "atom:type"); + mask = memory->grow(atom->mask, nmax, "atom:mask"); + image = memory->grow(atom->image, nmax, "atom:image"); + x = memory->grow(atom->x, nmax, 3, "atom:x"); + v = memory->grow(atom->v, nmax, 3, "atom:v"); + f = memory->grow(atom->f, nmax*comm->nthreads, 3, "atom:f"); + + rho = memory->grow(atom->rho, nmax, "atom:rho"); + drho = memory->grow(atom->drho, nmax*comm->nthreads, "atom:drho"); + vest = memory->grow(atom->vest, nmax, 3, "atom:vest"); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax); +} + +/* ---------------------------------------------------------------------- + reset local array ptrs + ------------------------------------------------------------------------- */ + +void AtomVecMDPD::grow_reset() { + tag = atom->tag; + type = atom->type; + mask = atom->mask; + image = atom->image; + x = atom->x; + v = atom->v; + f = atom->f; + rho = atom->rho; + drho = atom->drho; + vest = atom->vest; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecMDPD::copy(int i, int j, int delflag) { + //printf("in AtomVecMDPD::copy\n"); + tag[j] = tag[i]; + type[j] = type[i]; + mask[j] = mask[i]; + image[j] = image[i]; + x[j][0] = x[i][0]; + x[j][1] = x[i][1]; + x[j][2] = x[i][2]; + v[j][0] = v[i][0]; + v[j][1] = v[i][1]; + v[j][2] = v[i][2]; + + rho[j] = rho[i]; + drho[j] = drho[i]; + vest[j][0] = vest[i][0]; + vest[j][1] = vest[i][1]; + vest[j][2] = vest[i][2]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->copy_arrays(i, j,delflag); +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecMDPD::force_clear(int n, size_t nbytes) +{ + memset(&drho[n],0,nbytes); +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecMDPD::pack_comm_hybrid(int n, int *list, double *buf) { + //printf("in AtomVecMDPD::pack_comm_hybrid\n"); + int i, j, m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = rho[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecMDPD::unpack_comm_hybrid(int n, int first, double *buf) { + //printf("in AtomVecMDPD::unpack_comm_hybrid\n"); + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + rho[i] = buf[m++]; + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecMDPD::pack_border_hybrid(int n, int *list, double *buf) { + //printf("in AtomVecMDPD::pack_border_hybrid\n"); + int i, j, m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = rho[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecMDPD::unpack_border_hybrid(int n, int first, double *buf) { + //printf("in AtomVecMDPD::unpack_border_hybrid\n"); + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + rho[i] = buf[m++]; + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecMDPD::pack_reverse_hybrid(int n, int first, double *buf) { + //printf("in AtomVecMDPD::pack_reverse_hybrid\n"); + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + buf[m++] = drho[i]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecMDPD::unpack_reverse_hybrid(int n, int *list, double *buf) { + //printf("in AtomVecMDPD::unpack_reverse_hybrid\n"); + int i, j, m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + drho[j] += buf[m++]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecMDPD::pack_comm(int n, int *list, double *buf, int pbc_flag, + int *pbc) { + //printf("in AtomVecMDPD::pack_comm\n"); + int i, j, m; + double dx, dy, dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = rho[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0] * domain->xprd; + dy = pbc[1] * domain->yprd; + dz = pbc[2] * domain->zprd; + } else { + dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz; + dy = pbc[1] * domain->yprd + pbc[3] * domain->yz; + dz = pbc[2] * domain->zprd; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = rho[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecMDPD::pack_comm_vel(int n, int *list, double *buf, int pbc_flag, + int *pbc) { + //printf("in AtomVecMDPD::pack_comm_vel\n"); + int i, j, m; + double dx, dy, dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + buf[m++] = rho[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0] * domain->xprd; + dy = pbc[1] * domain->yprd; + dz = pbc[2] * domain->zprd; + } else { + dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz; + dy = pbc[1] * domain->yprd + pbc[3] * domain->yz; + dz = pbc[2] * domain->zprd; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + buf[m++] = rho[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecMDPD::unpack_comm(int n, int first, double *buf) { + //printf("in AtomVecMDPD::unpack_comm\n"); + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + rho[i] = buf[m++]; + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecMDPD::unpack_comm_vel(int n, int first, double *buf) { + //printf("in AtomVecMDPD::unpack_comm_vel\n"); + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + v[i][0] = buf[m++]; + v[i][1] = buf[m++]; + v[i][2] = buf[m++]; + rho[i] = buf[m++]; + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecMDPD::pack_reverse(int n, int first, double *buf) { + //printf("in AtomVecMDPD::pack_reverse\n"); + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + buf[m++] = f[i][0]; + buf[m++] = f[i][1]; + buf[m++] = f[i][2]; + buf[m++] = drho[i]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecMDPD::unpack_reverse(int n, int *list, double *buf) { + //printf("in AtomVecMDPD::unpack_reverse\n"); + int i, j, m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + f[j][0] += buf[m++]; + f[j][1] += buf[m++]; + f[j][2] += buf[m++]; + drho[j] += buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecMDPD::pack_border(int n, int *list, double *buf, int pbc_flag, + int *pbc) { + //printf("in AtomVecMDPD::pack_border\n"); + int i, j, m; + double dx, dy, dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = rho[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0] * domain->xprd; + dy = pbc[1] * domain->yprd; + dz = pbc[2] * domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = rho[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecMDPD::pack_border_vel(int n, int *list, double *buf, int pbc_flag, + int *pbc) +{ + int i,j,m; + double dx,dy,dz,dvx,dvy,dvz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + buf[m++] = rho[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0] * domain->xprd; + dy = pbc[1] * domain->yprd; + dz = pbc[2] * domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + buf[m++] = rho[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } else { + dvx = pbc[0] * h_rate[0] + pbc[5] * h_rate[5] + pbc[4] * h_rate[4]; + dvy = pbc[1] * h_rate[1] + pbc[3] * h_rate[3]; + dvz = pbc[2] * h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + if (mask[i] & deform_groupbit) { + buf[m++] = v[j][0] + dvx; + buf[m++] = v[j][1] + dvy; + buf[m++] = v[j][2] + dvz; + buf[m++] = rho[j]; + buf[m++] = vest[j][0] + dvx; + buf[m++] = vest[j][1] + dvy; + buf[m++] = vest[j][2] + dvz; + } else { + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + buf[m++] = rho[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecMDPD::unpack_border(int n, int first, double *buf) { + //printf("in AtomVecMDPD::unpack_border\n"); + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) + grow(0); + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + tag[i] = (tagint) ubuf(buf[m++]).i; + type[i] = (int) ubuf(buf[m++]).i; + mask[i] = (int) ubuf(buf[m++]).i; + rho[i] = buf[m++]; + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecMDPD::unpack_border_vel(int n, int first, double *buf) { + //printf("in AtomVecMDPD::unpack_border_vel\n"); + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) + grow(0); + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + tag[i] = (tagint) ubuf(buf[m++]).i; + type[i] = (int) ubuf(buf[m++]).i; + mask[i] = (int) ubuf(buf[m++]).i; + v[i][0] = buf[m++]; + v[i][1] = buf[m++]; + v[i][2] = buf[m++]; + rho[i] = buf[m++]; + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); +} + +/* ---------------------------------------------------------------------- + pack data for atom I for sending to another proc + xyz must be 1st 3 values, so comm::exchange() can test on them + ------------------------------------------------------------------------- */ + +int AtomVecMDPD::pack_exchange(int i, double *buf) { + //printf("in AtomVecMDPD::pack_exchange\n"); + int m = 1; + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + buf[m++] = v[i][0]; + buf[m++] = v[i][1]; + buf[m++] = v[i][2]; + buf[m++] = ubuf(tag[i]).d; + buf[m++] = ubuf(type[i]).d; + buf[m++] = ubuf(mask[i]).d; + buf[m++] = ubuf(image[i]).d; + buf[m++] = rho[i]; + buf[m++] = vest[i][0]; + buf[m++] = vest[i][1]; + buf[m++] = vest[i][2]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i, &buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecMDPD::unpack_exchange(double *buf) { + //printf("in AtomVecMDPD::unpack_exchange\n"); + int nlocal = atom->nlocal; + if (nlocal == nmax) + grow(0); + + int m = 1; + x[nlocal][0] = buf[m++]; + x[nlocal][1] = buf[m++]; + x[nlocal][2] = buf[m++]; + v[nlocal][0] = buf[m++]; + v[nlocal][1] = buf[m++]; + v[nlocal][2] = buf[m++]; + tag[nlocal] = (tagint) ubuf(buf[m++]).i; + type[nlocal] = (int) ubuf(buf[m++]).i; + mask[nlocal] = (int) ubuf(buf[m++]).i; + image[nlocal] = (imageint) ubuf(buf[m++]).i; + rho[nlocal] = buf[m++]; + vest[nlocal][0] = buf[m++]; + vest[nlocal][1] = buf[m++]; + vest[nlocal][2] = buf[m++]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]-> unpack_exchange(nlocal, + &buf[m]); + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + size of restart data for all atoms owned by this proc + include extra data stored by fixes + ------------------------------------------------------------------------- */ + +int AtomVecMDPD::size_restart() { + int i; + + int nlocal = atom->nlocal; + int n = 15 * nlocal; // 11 + rho + vest[3] + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + for (i = 0; i < nlocal; i++) + n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); + + return n; +} + +/* ---------------------------------------------------------------------- + pack atom I's data for restart file including extra quantities + xyz must be 1st 3 values, so that read_restart can test on them + molecular types may be negative, but write as positive + ------------------------------------------------------------------------- */ + +int AtomVecMDPD::pack_restart(int i, double *buf) { + int m = 1; + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + buf[m++] = ubuf(tag[i]).d; + buf[m++] = ubuf(type[i]).d; + buf[m++] = ubuf(mask[i]).d; + buf[m++] = ubuf(image[i]).d; + buf[m++] = v[i][0]; + buf[m++] = v[i][1]; + buf[m++] = v[i][2]; + buf[m++] = rho[i]; + buf[m++] = vest[i][0]; + buf[m++] = vest[i][1]; + buf[m++] = vest[i][2]; + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i, &buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- + unpack data for one atom from restart file including extra quantities + ------------------------------------------------------------------------- */ + +int AtomVecMDPD::unpack_restart(double *buf) { + int nlocal = atom->nlocal; + if (nlocal == nmax) { + grow(0); + if (atom->nextra_store) + memory->grow(atom->extra, nmax, atom->nextra_store, "atom:extra"); + } + + int m = 1; + x[nlocal][0] = buf[m++]; + x[nlocal][1] = buf[m++]; + x[nlocal][2] = buf[m++]; + tag[nlocal] = (tagint) ubuf(buf[m++]).i; + type[nlocal] = (int) ubuf(buf[m++]).i; + mask[nlocal] = (int) ubuf(buf[m++]).i; + image[nlocal] = (imageint) ubuf(buf[m++]).i; + v[nlocal][0] = buf[m++]; + v[nlocal][1] = buf[m++]; + v[nlocal][2] = buf[m++]; + rho[nlocal] = buf[m++]; + vest[nlocal][0] = buf[m++]; + vest[nlocal][1] = buf[m++]; + vest[nlocal][2] = buf[m++]; + + double **extra = atom->extra; + if (atom->nextra_store) { + int size = static_cast (buf[0]) - m; + for (int i = 0; i < size; i++) + extra[nlocal][i] = buf[m++]; + } + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + create one atom of itype at coord + set other values to defaults + ------------------------------------------------------------------------- */ + +void AtomVecMDPD::create_atom(int itype, double *coord) { + int nlocal = atom->nlocal; + if (nlocal == nmax) + grow(0); + + tag[nlocal] = 0; + type[nlocal] = itype; + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + mask[nlocal] = 1; + image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + rho[nlocal] = 0.0; + vest[nlocal][0] = 0.0; + vest[nlocal][1] = 0.0; + vest[nlocal][2] = 0.0; + drho[nlocal] = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack one line from Atoms section of data file + initialize other atom quantities + ------------------------------------------------------------------------- */ + +void AtomVecMDPD::data_atom(double *coord, imageint imagetmp, char **values) { + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + tag[nlocal] = ATOTAGINT(values[0]); + type[nlocal] = atoi(values[1]); + if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) + error->one(FLERR,"Invalid atom type in Atoms section of data file"); + + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + + image[nlocal] = imagetmp; + + mask[nlocal] = 1; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + + vest[nlocal][0] = 0.0; + vest[nlocal][1] = 0.0; + vest[nlocal][2] = 0.0; + + rho[nlocal] = 0.0; + drho[nlocal] = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack hybrid quantities from one line in Atoms section of data file + initialize other atom quantities for this sub-style + ------------------------------------------------------------------------- */ + +int AtomVecMDPD::data_atom_hybrid(int nlocal, char **values) +{ + rho[nlocal] = atof(values[0]); + return 3; +} + +/* ---------------------------------------------------------------------- + pack atom info for data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecMDPD::pack_data(double **buf) +{ + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + buf[i][0] = ubuf(tag[i]).d; + buf[i][1] = ubuf(type[i]).d; + buf[i][2] = rho[i]; + buf[i][3] = x[i][0]; + buf[i][4] = x[i][1]; + buf[i][5] = x[i][2]; + buf[i][6] = ubuf((image[i] & IMGMASK) - IMGMAX).d; + buf[i][7] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d; + buf[i][8] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d; + } +} + +/* ---------------------------------------------------------------------- + pack hybrid atom info for data file +------------------------------------------------------------------------- */ + +int AtomVecMDPD::pack_data_hybrid(int i, double *buf) +{ + buf[0] = rho[i]; + return 3; +} + +/* ---------------------------------------------------------------------- + write atom info to data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecMDPD::write_data(FILE *fp, int n, double **buf) +{ + for (int i = 0; i < n; i++) + fprintf(fp,TAGINT_FORMAT + " %d %-1.16e %-1.16e %-1.16e %-1.16e " + "%d %d %d\n", + (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i, + buf[i][2],buf[i][3],buf[i][4],buf[i][5], + (int) ubuf(buf[i][6]).i,(int) ubuf(buf[i][7]).i, + (int) ubuf(buf[i][8]).i); +} + +/* ---------------------------------------------------------------------- + write hybrid atom info to data file +------------------------------------------------------------------------- */ + +int AtomVecMDPD::write_data_hybrid(FILE *fp, double *buf) +{ + fprintf(fp," %-1.16e",buf[0]); + return 3; +} + +/* ---------------------------------------------------------------------- + assign an index to named atom property and return index + return -1 if name is unknown to this atom style +------------------------------------------------------------------------- */ + +int AtomVecMDPD::property_atom(char *name) +{ + if (strcmp(name,"rho") == 0) return 0; + if (strcmp(name,"drho") == 0) return 1; + return -1; +} + +/* ---------------------------------------------------------------------- + pack per-atom data into buf for ComputePropertyAtom + index maps to data specific to this atom style +------------------------------------------------------------------------- */ + +void AtomVecMDPD::pack_property_atom(int index, double *buf, + int nvalues, int groupbit) +{ + int *mask = atom->mask; + int nlocal = atom->nlocal; + int n = 0; + + if (index == 0) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = rho[i]; + else buf[n] = 0.0; + n += nvalues; + } + } else if (index == 1) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = drho[i]; + else buf[n] = 0.0; + n += nvalues; + } + } +} + +/* ---------------------------------------------------------------------- + return # of bytes of allocated memory + ------------------------------------------------------------------------- */ + +bigint AtomVecMDPD::memory_usage() { + bigint bytes = 0; + + if (atom->memcheck("tag")) bytes += memory->usage(tag, nmax); + if (atom->memcheck("type")) bytes += memory->usage(type, nmax); + if (atom->memcheck("mask")) bytes += memory->usage(mask, nmax); + if (atom->memcheck("image")) bytes += memory->usage(image, nmax); + if (atom->memcheck("x")) bytes += memory->usage(x, nmax, 3); + if (atom->memcheck("v")) bytes += memory->usage(v, nmax, 3); + if (atom->memcheck("f")) bytes += memory->usage(f, nmax*comm->nthreads, 3); + if (atom->memcheck("rho")) bytes += memory->usage(rho, nmax); + if (atom->memcheck("drho")) bytes += memory->usage(drho, nmax*comm->nthreads); + if (atom->memcheck("vest")) bytes += memory->usage(vest, nmax, 3); + + return bytes; +} diff --git a/src/USER-MESO/atom_vec_mdpd.h b/src/USER-MESO/atom_vec_mdpd.h new file mode 100644 index 0000000000..9e9ffcdcf2 --- /dev/null +++ b/src/USER-MESO/atom_vec_mdpd.h @@ -0,0 +1,79 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef ATOM_CLASS + +AtomStyle(mdpd,AtomVecMDPD) + +#else + +#ifndef LMP_ATOM_VEC_MDPD_H +#define LMP_ATOM_VEC_MDPD_H + +#include "atom_vec.h" + +namespace LAMMPS_NS { + +class AtomVecMDPD : public AtomVec { + public: + AtomVecMDPD(class LAMMPS *); + ~AtomVecMDPD() {} + void grow(int); + void grow_reset(); + void copy(int, int, int); + void force_clear(int, size_t); + int pack_comm(int, int *, double *, int, int *); + int pack_comm_vel(int, int *, double *, int, int *); + void unpack_comm(int, int, double *); + void unpack_comm_vel(int, int, double *); + int pack_reverse(int, int, double *); + void unpack_reverse(int, int *, double *); + int pack_comm_hybrid(int, int *, double *); + int unpack_comm_hybrid(int, int, double *); + int pack_border_hybrid(int, int *, double *); + int unpack_border_hybrid(int, int, double *); + int pack_reverse_hybrid(int, int, double *); + int unpack_reverse_hybrid(int, int *, double *); + int pack_border(int, int *, double *, int, int *); + int pack_border_vel(int, int *, double *, int, int *); + void unpack_border(int, int, double *); + void unpack_border_vel(int, int, double *); + int pack_exchange(int, double *); + int unpack_exchange(double *); + int size_restart(); + int pack_restart(int, double *); + int unpack_restart(double *); + void create_atom(int, double *); + void data_atom(double *, imageint, char **); + int data_atom_hybrid(int, char **); + void pack_data(double **); + int pack_data_hybrid(int, double *); + void write_data(FILE *, int, double **); + int write_data_hybrid(FILE *, double *); + int property_atom(char *); + void pack_property_atom(int, double *, int, int); + bigint memory_usage(); + + private: + tagint *tag; + int *type,*mask; + imageint *image; + double **x,**v,**f; + double *rho, *drho; + double **vest; // estimated velocity during force computation +}; + +} + +#endif +#endif diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESO/atom_vec_tdpd.cpp new file mode 100644 index 0000000000..ce9e492029 --- /dev/null +++ b/src/USER-MESO/atom_vec_tdpd.cpp @@ -0,0 +1,879 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include "atom_vec_tdpd.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "domain.h" +#include "modify.h" +#include "fix.h" +#include "update.h" +#include "memory.h" +#include "error.h" +#include "input.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +AtomVecTDPD::AtomVecTDPD(LAMMPS *lmp) : AtomVec(lmp) +{ + if(strcmp(update->unit_style,"lj") != 0) + error->all(FLERR,"Atom style edpd requires lj units"); + + molecular = 0; + mass_type = 1; + forceclearflag = 1; + + comm_x_only = comm_f_only = 0; + comm->ghost_velocity = 1; + + cc_species = 0; // for now, reset in process_args() + + size_forward = 3 + cc_species + 3; //vest[3] + size_reverse = 3 + cc_species; + size_border = 6 + cc_species + 3; //vest[3] + size_velocity = 3; + // for data_atom, we read id + type + xyz[3] + cc[i] where i=1,cc_species + size_data_atom = 5 + cc_species; + size_data_vel = 4; + xcol_data = 3; + + atom->tdpd_flag = 1; + atom->vest_flag = 1; +} + +/* ---------------------------------------------------------------------- + process additional args + single arg = number of cc_species +------------------------------------------------------------------------- */ + +void AtomVecTDPD::process_args(int narg, char **arg) +{ + if (narg < 1) error->all(FLERR,"Invalid atom_style tdpd command"); + + atom->cc_species = force->inumeric(FLERR,arg[0]); + cc_species = atom->cc_species; + + // reset sizes that depend on cc_species + + size_forward = 3 + cc_species + 3; + size_reverse = 3 + cc_species; + size_border = 6 + cc_species + 3; + size_data_atom = 5 + cc_species; +} + +/* ---------------------------------------------------------------------- + grow atom arrays + n = 0 grows arrays by a chunk + n > 0 allocates arrays to size n +------------------------------------------------------------------------- */ + +void AtomVecTDPD::grow(int n) +{ + if (n == 0) grow_nmax(); + else nmax = n; + atom->nmax = nmax; + if (nmax < 0 || nmax > MAXSMALLINT) + error->one(FLERR,"Per-processor system is too big"); + + tag = memory->grow(atom->tag,nmax,"atom:tag"); + type = memory->grow(atom->type,nmax,"atom:type"); + mask = memory->grow(atom->mask,nmax,"atom:mask"); + image = memory->grow(atom->image,nmax,"atom:image"); + x = memory->grow(atom->x,nmax,3,"atom:x"); + v = memory->grow(atom->v,nmax,3,"atom:v"); + f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f"); + cc = memory->grow(atom->cc,nmax*comm->nthreads,cc_species,"atom:cc"); + cc_flux = memory->grow(atom->cc_flux,nmax*comm->nthreads,cc_species, + "atom:cc_flux"); + vest = memory->grow(atom->vest, nmax, 3, "atom:vest"); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax); +} + +/* ---------------------------------------------------------------------- + reset local array ptrs +------------------------------------------------------------------------- */ + +void AtomVecTDPD::grow_reset() +{ + tag = atom->tag; type = atom->type; + mask = atom->mask; image = atom->image; + x = atom->x; v = atom->v; f = atom->f; + cc = atom->cc; cc_flux = atom->cc_flux; + vest = atom->vest; +} + +/* ---------------------------------------------------------------------- + copy atom I info to atom J +------------------------------------------------------------------------- */ + +void AtomVecTDPD::copy(int i, int j, int delflag) +{ + tag[j] = tag[i]; + type[j] = type[i]; + mask[j] = mask[i]; + image[j] = image[i]; + x[j][0] = x[i][0]; + x[j][1] = x[i][1]; + x[j][2] = x[i][2]; + v[j][0] = v[i][0]; + v[j][1] = v[i][1]; + v[j][2] = v[i][2]; + + for(int k = 0; k < cc_species; k++) + cc[j][k] = cc[i][k]; + + vest[j][0] = vest[i][0]; + vest[j][1] = vest[i][1]; + vest[j][2] = vest[i][2]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); +} + + +void AtomVecTDPD::force_clear(int n, size_t nbytes) +{ + memset(&cc_flux[n][0],0,cc_species*nbytes); +} + + +/* ---------------------------------------------------------------------- */ + +int AtomVecTDPD::pack_comm(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,k,m; + double dx,dy,dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + + for(k = 0; k < cc_species; k++) + buf[m++] = cc[j][k]; + + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; + dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; + dz = pbc[2]*domain->zprd; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + + for(k = 0; k < cc_species; k++) + buf[m++] = cc[j][k]; + + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecTDPD::pack_comm_vel(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,k,m; + double dx,dy,dz,dvx,dvy,dvz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + + for(k = 0; k < cc_species; k++) + buf[m++] = cc[j][k]; + + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; + dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; + dz = pbc[2]*domain->zprd; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + + for(k = 0; k < cc_species; k++) + buf[m++] = cc[j][k]; + + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + if (mask[i] & deform_groupbit) { + buf[m++] = v[j][0] + dvx; + buf[m++] = v[j][1] + dvy; + buf[m++] = v[j][2] + dvz; + } else { + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + for(k = 0; k < cc_species; k++) + buf[m++] = cc[j][k]; + + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecTDPD::unpack_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + + for(int k = 0; k < cc_species; k++) + cc[i][k] = buf[m++]; + + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecTDPD::unpack_comm_vel(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + v[i][0] = buf[m++]; + v[i][1] = buf[m++]; + v[i][2] = buf[m++]; + for(int k = 0; k < cc_species; k++) + cc[i][k] = buf[m++]; + + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecTDPD::pack_reverse(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + buf[m++] = f[i][0]; + buf[m++] = f[i][1]; + buf[m++] = f[i][2]; + for(int k = 0; k < cc_species; k++) + buf[m++] = cc_flux[i][k]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecTDPD::unpack_reverse(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + f[j][0] += buf[m++]; + f[j][1] += buf[m++]; + f[j][2] += buf[m++]; + for(int k = 0; k < cc_species; k++) + cc_flux[j][k] += buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecTDPD::pack_border(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + for(int k = 0; k < cc_species; k++) + buf[m++] = cc[j][k]; + + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + for(int k = 0; k < cc_species; k++) + buf[m++] = cc[j][k]; + + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecTDPD::pack_border_vel(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz,dvx,dvy,dvz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + for(int k = 0; k < cc_species; k++) + buf[m++] = cc[j][k]; + + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + for(int k = 0; k < cc_species; k++) + buf[m++] = cc[j][k]; + + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + if (mask[i] & deform_groupbit) { + buf[m++] = v[j][0] + dvx; + buf[m++] = v[j][1] + dvy; + buf[m++] = v[j][2] + dvz; + } else { + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + for(int k = 0; k < cc_species; k++) + buf[m++] = cc[j][k]; + + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + } + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecTDPD::unpack_border(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) grow(0); + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + tag[i] = (tagint) ubuf(buf[m++]).i; + type[i] = (int) ubuf(buf[m++]).i; + mask[i] = (int) ubuf(buf[m++]).i; + for(int k = 0; k < cc_species; k++) + cc[i][k] = buf[m++]; + + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecTDPD::unpack_border_vel(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) grow(0); + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + tag[i] = (tagint) ubuf(buf[m++]).i; + type[i] = (int) ubuf(buf[m++]).i; + mask[i] = (int) ubuf(buf[m++]).i; + v[i][0] = buf[m++]; + v[i][1] = buf[m++]; + v[i][2] = buf[m++]; + for(int k = 0; k < cc_species; k++) + cc[i][k] = buf[m++]; + + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); +} + +/* ---------------------------------------------------------------------- + pack data for atom I for sending to another proc + xyz must be 1st 3 values, so comm::exchange() can test on them +------------------------------------------------------------------------- */ + +int AtomVecTDPD::pack_exchange(int i, double *buf) +{ + int m = 1; + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + buf[m++] = v[i][0]; + buf[m++] = v[i][1]; + buf[m++] = v[i][2]; + buf[m++] = ubuf(tag[i]).d; + buf[m++] = ubuf(type[i]).d; + buf[m++] = ubuf(mask[i]).d; + buf[m++] = ubuf(image[i]).d; + for(int k = 0; k < cc_species; k++) + buf[m++] = cc[i][k]; + + buf[m++] = vest[i][0]; + buf[m++] = vest[i][1]; + buf[m++] = vest[i][2]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecTDPD::unpack_exchange(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + int m = 1; + x[nlocal][0] = buf[m++]; + x[nlocal][1] = buf[m++]; + x[nlocal][2] = buf[m++]; + v[nlocal][0] = buf[m++]; + v[nlocal][1] = buf[m++]; + v[nlocal][2] = buf[m++]; + tag[nlocal] = (tagint) ubuf(buf[m++]).i; + type[nlocal] = (int) ubuf(buf[m++]).i; + mask[nlocal] = (int) ubuf(buf[m++]).i; + image[nlocal] = (imageint) ubuf(buf[m++]).i; + for(int k = 0; k < cc_species; k++) + cc[nlocal][k] = buf[m++]; + + vest[nlocal][0] = buf[m++]; + vest[nlocal][1] = buf[m++]; + vest[nlocal][2] = buf[m++]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]-> + unpack_exchange(nlocal,&buf[m]); + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + size of restart data for all atoms owned by this proc + include extra data stored by fixes +------------------------------------------------------------------------- */ + +int AtomVecTDPD::size_restart() +{ + int i; + + int nlocal = atom->nlocal; + int n = (11 + cc_species + 3) * nlocal; // 11 + cc[i] + vest[3] + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + for (i = 0; i < nlocal; i++) + n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); + + return n; +} + +/* ---------------------------------------------------------------------- + pack atom I's data for restart file including extra quantities + xyz must be 1st 3 values, so that read_restart can test on them + molecular types may be negative, but write as positive +------------------------------------------------------------------------- */ + +int AtomVecTDPD::pack_restart(int i, double *buf) +{ + int m = 1; + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + buf[m++] = ubuf(tag[i]).d; + buf[m++] = ubuf(type[i]).d; + buf[m++] = ubuf(mask[i]).d; + buf[m++] = ubuf(image[i]).d; + buf[m++] = v[i][0]; + buf[m++] = v[i][1]; + buf[m++] = v[i][2]; + for(int k = 0; k < cc_species; k++) + buf[m++] = cc[i][k]; + + buf[m++] = vest[i][0]; + buf[m++] = vest[i][1]; + buf[m++] = vest[i][2]; + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- + unpack data for one atom from restart file including extra quantities +------------------------------------------------------------------------- */ + +int AtomVecTDPD::unpack_restart(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) { + grow(0); + if (atom->nextra_store) + memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); + } + + int m = 1; + x[nlocal][0] = buf[m++]; + x[nlocal][1] = buf[m++]; + x[nlocal][2] = buf[m++]; + tag[nlocal] = (tagint) ubuf(buf[m++]).i; + type[nlocal] = (int) ubuf(buf[m++]).i; + mask[nlocal] = (int) ubuf(buf[m++]).i; + image[nlocal] = (imageint) ubuf(buf[m++]).i; + v[nlocal][0] = buf[m++]; + v[nlocal][1] = buf[m++]; + v[nlocal][2] = buf[m++]; + for(int k = 0; k < cc_species; k++) + cc[nlocal][k] = buf[m++]; + + vest[nlocal][0] = buf[m++]; + vest[nlocal][1] = buf[m++]; + vest[nlocal][2] = buf[m++]; + + double **extra = atom->extra; + if (atom->nextra_store) { + int size = static_cast (buf[0]) - m; + for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; + } + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + create one atom of itype at coord + set other values to defaults +------------------------------------------------------------------------- */ + +void AtomVecTDPD::create_atom(int itype, double *coord) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + tag[nlocal] = 0; + type[nlocal] = itype; + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + mask[nlocal] = 1; + image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + + for(int k = 0; k < cc_species; k++) + cc[nlocal][k] = 0.0; + + vest[nlocal][0] = 0.0; + vest[nlocal][1] = 0.0; + vest[nlocal][2] = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack one line from Atoms section of data file + initialize other atom quantities +------------------------------------------------------------------------- */ + +void AtomVecTDPD::data_atom(double *coord, imageint imagetmp, char **values) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + tag[nlocal] = ATOTAGINT(values[0]); + type[nlocal] = atoi(values[1]); + if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) + error->one(FLERR,"Invalid atom type in Atoms section of data file"); + + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + + for(int k = 0; k < cc_species; k++) + cc[nlocal][k] = atof( values[5+k] ); + + image[nlocal] = imagetmp; + + mask[nlocal] = 1; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + + vest[nlocal][0] = 0.0; + vest[nlocal][1] = 0.0; + vest[nlocal][2] = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + pack atom info for data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecTDPD::pack_data(double **buf) +{ + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + buf[i][0] = ubuf(tag[i]).d; + buf[i][1] = ubuf(type[i]).d; + buf[i][2] = x[i][0]; + buf[i][3] = x[i][1]; + buf[i][4] = x[i][2]; + buf[i][5] = ubuf((image[i] & IMGMASK) - IMGMAX).d; + buf[i][6] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d; + buf[i][7] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d; + for(int k = 0; k < cc_species; k++) + buf[i][8+k] = cc[i][k]; + } +} + +/* ---------------------------------------------------------------------- + write atom info to data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecTDPD::write_data(FILE *fp, int n, double **buf) +{ + for (int i = 0; i < n; i++){ + fprintf(fp,TAGINT_FORMAT " %d %-1.16e %-1.16e %-1.16e %d %d %d", + (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i, + buf[i][2],buf[i][3],buf[i][4], + (int) ubuf(buf[i][5]).i,(int) ubuf(buf[i][6]).i, + (int) ubuf(buf[i][7]).i); + for(int k = 0; k < cc_species; k++) + fprintf(fp,TAGINT_FORMAT " %-1.16e",buf[i][8+k]); + fprintf(fp,TAGINT_FORMAT "\n"); + } +} + +/* ---------------------------------------------------------------------- + return # of bytes of allocated memory +------------------------------------------------------------------------- */ + +bigint AtomVecTDPD::memory_usage() +{ + bigint bytes = 0; + + if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); + if (atom->memcheck("type")) bytes += memory->usage(type,nmax); + if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); + if (atom->memcheck("image")) bytes += memory->usage(image,nmax); + if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); + if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); + if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3); + if (atom->memcheck("cc")) bytes += memory->usage(cc,nmax*comm->nthreads,cc_species); + if (atom->memcheck("cc_flux")) bytes += memory->usage(cc_flux,nmax*comm->nthreads,cc_species); + if (atom->memcheck("vest")) bytes += memory->usage(vest, nmax); + + return bytes; +} diff --git a/src/USER-MESO/atom_vec_tdpd.h b/src/USER-MESO/atom_vec_tdpd.h new file mode 100644 index 0000000000..86e9ae4bb8 --- /dev/null +++ b/src/USER-MESO/atom_vec_tdpd.h @@ -0,0 +1,83 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef ATOM_CLASS + +AtomStyle(tdpd,AtomVecTDPD) + +#else + +#ifndef LMP_ATOM_VEC_TDPD_H +#define LMP_ATOM_VEC_TDPD_H + +#include "atom_vec.h" + +namespace LAMMPS_NS { + +class AtomVecTDPD : public AtomVec { + public: + AtomVecTDPD(class LAMMPS *); + virtual ~AtomVecTDPD() {} + void process_args(int, char **); + void grow(int); + void grow_reset(); + void copy(int, int, int); + void force_clear(int, size_t); + virtual int pack_comm(int, int *, double *, int, int *); + virtual int pack_comm_vel(int, int *, double *, int, int *); + virtual void unpack_comm(int, int, double *); + virtual void unpack_comm_vel(int, int, double *); + int pack_reverse(int, int, double *); + void unpack_reverse(int, int *, double *); + virtual int pack_border(int, int *, double *, int, int *); + virtual int pack_border_vel(int, int *, double *, int, int *); + virtual void unpack_border(int, int, double *); + virtual void unpack_border_vel(int, int, double *); + virtual int pack_exchange(int, double *); + virtual int unpack_exchange(double *); + int size_restart(); + int pack_restart(int, double *); + int unpack_restart(double *); + void create_atom(int, double *); + void data_atom(double *, imageint, char **); + void pack_data(double **); + void write_data(FILE *, int, double **); + bigint memory_usage(); + + protected: + tagint *tag; + int *type,*mask; + imageint *image; + double **x,**v,**f; + double **vest; // store intermediate velocity for using mvv integrator + double **cc,**cc_flux; + int cc_species; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Per-processor system is too big + +The number of owned atoms plus ghost atoms on a single +processor must fit in 32-bit integer. + +E: Invalid atom type in Atoms section of data file + +Atom types must range from 1 to specified # of types. + +*/ diff --git a/src/USER-MESO/compute_edpd_temp_atom.cpp b/src/USER-MESO/compute_edpd_temp_atom.cpp new file mode 100644 index 0000000000..15fdab2a69 --- /dev/null +++ b/src/USER-MESO/compute_edpd_temp_atom.cpp @@ -0,0 +1,97 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "compute_edpd_temp_atom.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeEDPDTempAtom::ComputeEDPDTempAtom(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Number of arguments for compute edpd/temp/atom command != 3"); + if (atom->edpd_flag != 1) error->all(FLERR,"compute edpd/temp/atom command requires atom_style with temperature (e.g. edpd)"); + + peratom_flag = 1; + size_peratom_cols = 0; + + nmax = 0; + temp_vector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeEDPDTempAtom::~ComputeEDPDTempAtom() +{ + memory->sfree(temp_vector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeEDPDTempAtom::init() +{ + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style,"temp_vector/atom") == 0) count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR,"More than one compute temp_vector/atom"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeEDPDTempAtom::compute_peratom() +{ + invoked_peratom = update->ntimestep; + + // grow temp_vector array if necessary + + if (atom->nmax > nmax) { + memory->sfree(temp_vector); + nmax = atom->nmax; + temp_vector = (double *) memory->smalloc(nmax*sizeof(double),"temp_vector/atom:temp_vector"); + vector_atom = temp_vector; + } + + double *edpd_temp = atom->edpd_temp; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + temp_vector[i] = edpd_temp[i]; + } + else { + temp_vector[i] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +double ComputeEDPDTempAtom::memory_usage() +{ + double bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-MESO/compute_edpd_temp_atom.h b/src/USER-MESO/compute_edpd_temp_atom.h new file mode 100644 index 0000000000..4c61b664cc --- /dev/null +++ b/src/USER-MESO/compute_edpd_temp_atom.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(edpd/temp/atom,ComputeEDPDTempAtom) + +#else + +#ifndef LMP_COMPUTE_EDPD_TEMP_ATOM_H +#define LMP_COMPUTE_EDPD_TEMP_ATOM_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeEDPDTempAtom : public Compute { + public: + ComputeEDPDTempAtom(class LAMMPS *, int, char **); + ~ComputeEDPDTempAtom(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double *temp_vector; +}; + +} + +#endif +#endif diff --git a/src/USER-MESO/compute_tdpd_cc_atom.cpp b/src/USER-MESO/compute_tdpd_cc_atom.cpp new file mode 100644 index 0000000000..b33550f5c1 --- /dev/null +++ b/src/USER-MESO/compute_tdpd_cc_atom.cpp @@ -0,0 +1,98 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "compute_tdpd_cc_atom.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeTDPDCCAtom::ComputeTDPDCCAtom(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 4) error->all(FLERR,"Number of arguments for compute tdpd/cc/atom command != 4"); + if (atom->tdpd_flag != 1) error->all(FLERR,"compute tdpd/cc/atom command requires atom_style with concentration (e.g. tdpd)"); + + index = force->inumeric(FLERR,arg[3]); + + peratom_flag = 1; + size_peratom_cols = 0; + + nmax = 0; + cc_vector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeTDPDCCAtom::~ComputeTDPDCCAtom() +{ + memory->sfree(cc_vector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeTDPDCCAtom::init() +{ + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style,"cc_vector/atom") == 0) count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR,"More than one compute cc_vector/atom"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeTDPDCCAtom::compute_peratom() +{ + invoked_peratom = update->ntimestep; + + // grow cc_vector array if necessary + + if (atom->nmax > nmax) { + memory->sfree(cc_vector); + nmax = atom->nmax; + cc_vector = (double *) memory->smalloc(nmax*sizeof(double),"cc_vector/atom:cc_vector"); + vector_atom = cc_vector; + } + + double **cc = atom->cc; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + cc_vector[i] = cc[i][index-1]; + } + else + cc_vector[i] = 0.0; + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +double ComputeTDPDCCAtom::memory_usage() +{ + double bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-MESO/compute_tdpd_cc_atom.h b/src/USER-MESO/compute_tdpd_cc_atom.h new file mode 100644 index 0000000000..324cb779a4 --- /dev/null +++ b/src/USER-MESO/compute_tdpd_cc_atom.h @@ -0,0 +1,44 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(tdpd/cc/atom,ComputeTDPDCCAtom) + +#else + +#ifndef LMP_COMPUTE_TDPD_CC_ATOM_H +#define LMP_COMPUTE_TDPD_CC_ATOM_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeTDPDCCAtom : public Compute { + public: + ComputeTDPDCCAtom(class LAMMPS *, int, char **); + ~ComputeTDPDCCAtom(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + int index; + double *cc_vector; +}; + +} + +#endif +#endif diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESO/fix_edpd_source.cpp new file mode 100644 index 0000000000..3ee7e8e291 --- /dev/null +++ b/src/USER-MESO/fix_edpd_source.cpp @@ -0,0 +1,120 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include "fix_edpd_source.h" +#include "atom.h" +#include "comm.h" +#include "update.h" +#include "modify.h" +#include "domain.h" +#include "lattice.h" +#include "input.h" +#include "variable.h" +#include "error.h" +#include "force.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixEDPDSource::FixEDPDSource(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (strcmp(style,"edpd/source") != 0 && narg < 4) + error->all(FLERR,"Illegal fix edpd/source command"); + + int iarg = 3; + + if (strcmp(arg[iarg],"sphere") == 0) option = 0; + else if (strcmp(arg[iarg],"cuboid") == 0) option = 1; + else error->all(FLERR,"Illegal fix edpd/source command"); + iarg++; + + if(option == 0){ + if (narg != 9 ) error->all(FLERR,"Illegal fix edpd/source command (5 args for sphere)"); + center[0] = force->numeric(FLERR,arg[iarg++]); + center[1] = force->numeric(FLERR,arg[iarg++]); + center[2] = force->numeric(FLERR,arg[iarg++]); + radius = force->numeric(FLERR,arg[iarg++]); + value = force->numeric(FLERR,arg[iarg++]); + } + else if(option == 1){ + if (narg != 11 ) error->all(FLERR,"Illegal fix edpd/edpd command (7 args for cuboid)"); + center[0] = force->numeric(FLERR,arg[iarg++]); + center[1] = force->numeric(FLERR,arg[iarg++]); + center[2] = force->numeric(FLERR,arg[iarg++]); + dLx = force->numeric(FLERR,arg[iarg++]); + dLy = force->numeric(FLERR,arg[iarg++]); + dLz = force->numeric(FLERR,arg[iarg++]); + value = force->numeric(FLERR,arg[iarg++]); + } + else error->all(FLERR,"Illegal fix edpd/source command"); +} + +/* ---------------------------------------------------------------------- */ + +FixEDPDSource::~FixEDPDSource() +{ +} + +/* ---------------------------------------------------------------------- */ + +int FixEDPDSource::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixEDPDSource::init() +{ +} + +/* ---------------------------------------------------------------------- */ + +void FixEDPDSource::post_force(int vflag) +{ + double **x = atom->x; + double *edpd_flux = atom->edpd_flux; + double *edpd_cv = atom->edpd_cv; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + double drx, dry, drz, rsq; + double radius_sq = radius*radius*radius; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + if(option == 0){ + drx = x[i][0] - center[0]; + dry = x[i][1] - center[1]; + drz = x[i][2] - center[2]; + rsq = drx*drx + dry*dry + drz*drz; + if(rsq < radius_sq) + edpd_flux[i] += value*edpd_cv[i]; + } + else if(option == 1){ + drx = x[i][0] - center[0]; + dry = x[i][1] - center[1]; + drz = x[i][2] - center[2]; + if(abs(drx) <= 0.5*dLx && abs(dry) <= 0.5*dLy && abs(drz) <= 0.5*dLz) + edpd_flux[i] += value*edpd_cv[i]; + } + } + } +} diff --git a/src/USER-MESO/fix_edpd_source.h b/src/USER-MESO/fix_edpd_source.h new file mode 100644 index 0000000000..1ea8610ce9 --- /dev/null +++ b/src/USER-MESO/fix_edpd_source.h @@ -0,0 +1,44 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(edpd/source,FixEDPDSource) + +#else + +#ifndef LMP_FIX_EDPDSOURCE_H +#define LMP_FIX_EDPDSOURCE_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixEDPDSource : public Fix { + public: + FixEDPDSource(class LAMMPS *, int, char **); + ~FixEDPDSource(); + int setmask(); + void init(); + void post_force(int); + + protected: + int option; + double center[3], radius, dLx, dLy, dLz; + double value; +}; + +} + +#endif +#endif diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESO/fix_mvv_dpd.cpp new file mode 100644 index 0000000000..77a67273f6 --- /dev/null +++ b/src/USER-MESO/fix_mvv_dpd.cpp @@ -0,0 +1,136 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This is a time integrator for position and velocity (x and v) using the + modified velocity-Verlet (MVV) algorithm. + Setting verlet = 0.5 recovers the standard velocity-Verlet algorithm. + + Contributing author: Zhen Li (Brown University) + Email: zhen_li@brown.edu +------------------------------------------------------------------------- */ + +#include +#include +#include "fix_mvv_dpd.h" +#include "atom.h" +#include "force.h" +#include "update.h" +#include "respa.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixMvvDPD::FixMvvDPD(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (strcmp(style,"mvv/dpd") != 0 && narg < 3) + error->all(FLERR,"Illegal fix mvv/dpd command"); + + verlet = 0.5; + if(narg > 3) verlet = force->numeric(FLERR,arg[3]); + + dynamic_group_allow = 1; + time_integrate = 1; +} + +/* ---------------------------------------------------------------------- */ + +int FixMvvDPD::setmask() +{ + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= FINAL_INTEGRATE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixMvvDPD::init() +{ + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; +} + +/* ---------------------------------------------------------------------- + allow for both per-type and per-atom mass +------------------------------------------------------------------------- */ + +void FixMvvDPD::initial_integrate(int vflag) +{ + double dtfm; + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double **vest = atom->vest; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (rmass) dtfm = dtf / rmass[i]; + else dtfm = dtf / mass[type[i]]; + + vest[i][0] = v[i][0] + dtfm * f[i][0]; + vest[i][1] = v[i][1] + dtfm * f[i][1]; + vest[i][2] = v[i][2] + dtfm * f[i][2]; + + x[i][0] += dtv * vest[i][0]; + x[i][1] += dtv * vest[i][1]; + x[i][2] += dtv * vest[i][2]; + v[i][0] += 2.0 * verlet * dtfm * f[i][0]; + v[i][1] += 2.0 * verlet * dtfm * f[i][1]; + v[i][2] += 2.0 * verlet * dtfm * f[i][2]; + } +} + +/* ---------------------------------------------------------------------- */ + +void FixMvvDPD::final_integrate() +{ + double dtfm; + double **v = atom->v; + double **f = atom->f; + double **vest = atom->vest; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (rmass) dtfm = dtf / rmass[i]; + else dtfm = dtf / mass[type[i]]; + + v[i][0] = vest[i][0] + dtfm * f[i][0]; + v[i][1] = vest[i][1] + dtfm * f[i][1]; + v[i][2] = vest[i][2] + dtfm * f[i][2]; + } +} + +/* ---------------------------------------------------------------------- */ + +void FixMvvDPD::reset_dt() +{ + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; +} diff --git a/src/USER-MESO/fix_mvv_dpd.h b/src/USER-MESO/fix_mvv_dpd.h new file mode 100644 index 0000000000..86cc79485f --- /dev/null +++ b/src/USER-MESO/fix_mvv_dpd.h @@ -0,0 +1,45 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(mvv/dpd,FixMvvDPD) + +#else + +#ifndef LMP_FIX_MVV_DPD_H +#define LMP_FIX_MVV_DPD_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixMvvDPD : public Fix { + public: + FixMvvDPD(class LAMMPS *, int, char **); + virtual ~FixMvvDPD() {} + int setmask(); + virtual void init(); + virtual void initial_integrate(int); + virtual void final_integrate(); + virtual void reset_dt(); + + protected: + double dtv, dtf; + double verlet; +}; + +} + +#endif +#endif diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESO/fix_mvv_edpd.cpp new file mode 100644 index 0000000000..fe801d6d36 --- /dev/null +++ b/src/USER-MESO/fix_mvv_edpd.cpp @@ -0,0 +1,163 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This is a time integrator for position, velocity and temperature (x, + v and edpd_T) using the modified velocity-Verlet (MVV) algorithm. + Setting verlet = 0.5 recovers the standard velocity-Verlet algorithm. + + Contributing author: Zhen Li (Brown University) + Email: zhen_li@brown.edu + + Please cite the related publication: + Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. "Energy- + conserving dissipative particle dynamics with temperature-dependent + properties". Journal of Computational Physics, 2014, 265: 113-127. + + Z. Li, Y.-H. Tang , X. Li and G.E. Karniadakis. "Mesoscale modeling of + phase transition dynamics of thermoresponsive polymers". Chemical + Communications, 2015, 51: 11038-11040. +------------------------------------------------------------------------- */ + +#include +#include +#include "fix_mvv_edpd.h" +#include "atom.h" +#include "force.h" +#include "update.h" +#include "respa.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixMvvEDPD::FixMvvEDPD(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (strcmp(style,"mvv/edpd") != 0 && narg < 3) + error->all(FLERR,"Illegal fix mvv/edpd command"); + + verlet = 0.5; + if(narg > 3) verlet = force->numeric(FLERR,arg[3]); + + dynamic_group_allow = 1; + time_integrate = 1; +} + +/* ---------------------------------------------------------------------- */ + +int FixMvvEDPD::setmask() +{ + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= FINAL_INTEGRATE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixMvvEDPD::init() +{ + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; +} + +/* ---------------------------------------------------------------------- + allow for both per-type and per-atom mass +------------------------------------------------------------------------- */ + +void FixMvvEDPD::initial_integrate(int vflag) +{ + double dtfm,dtT; + // update v and x and cc of atoms in group + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double *edpd_temp = atom->edpd_temp; + double *edpd_flux = atom->edpd_flux; + double *edpd_cv = atom->edpd_cv; + double **vest = atom->vest; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (rmass) dtfm = dtf / rmass[i]; + else dtfm = dtf / mass[type[i]]; + + dtT = 0.5 * dtv / edpd_cv[i]; + + vest[i][0] = v[i][0] + dtfm * f[i][0]; + vest[i][1] = v[i][1] + dtfm * f[i][1]; + vest[i][2] = v[i][2] + dtfm * f[i][2]; + vest[i][3] = edpd_temp[i] + dtT * edpd_flux[i]; + + x[i][0] += dtv * vest[i][0]; + x[i][1] += dtv * vest[i][1]; + x[i][2] += dtv * vest[i][2]; + v[i][0] += 2.0 * verlet * dtfm * f[i][0]; + v[i][1] += 2.0 * verlet * dtfm * f[i][1]; + v[i][2] += 2.0 * verlet * dtfm * f[i][2]; + edpd_temp[i] += 2.0 * verlet * dtT * edpd_flux[i]; + } +} + +/* ---------------------------------------------------------------------- */ + +void FixMvvEDPD::final_integrate() +{ + double dtfm, dtT; + + // update v and edpd_temp of atoms in group + + double **v = atom->v; + double **f = atom->f; + double *edpd_temp = atom->edpd_temp; + double *edpd_flux = atom->edpd_flux; + double *edpd_cv = atom->edpd_cv; + double **vest = atom->vest; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (rmass) dtfm = dtf / rmass[i]; + else dtfm = dtf / mass[type[i]]; + + dtT = 0.5 * dtv / edpd_cv[i]; + + v[i][0] = vest[i][0] + dtfm * f[i][0]; + v[i][1] = vest[i][1] + dtfm * f[i][1]; + v[i][2] = vest[i][2] + dtfm * f[i][2]; + edpd_temp[i] = vest[i][3] + dtT * edpd_flux[i]; + } +} + +/* ---------------------------------------------------------------------- */ + +void FixMvvEDPD::reset_dt() +{ + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; +} diff --git a/src/USER-MESO/fix_mvv_edpd.h b/src/USER-MESO/fix_mvv_edpd.h new file mode 100644 index 0000000000..0d9c5f195a --- /dev/null +++ b/src/USER-MESO/fix_mvv_edpd.h @@ -0,0 +1,45 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(mvv/edpd,FixMvvEDPD) + +#else + +#ifndef LMP_FIX_MVV_EDPD_H +#define LMP_FIX_MVV_EDPD_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixMvvEDPD : public Fix { + public: + FixMvvEDPD(class LAMMPS *, int, char **); + virtual ~FixMvvEDPD() {} + int setmask(); + virtual void init(); + virtual void initial_integrate(int); + virtual void final_integrate(); + virtual void reset_dt(); + + protected: + double dtv, dtf; + double verlet; +}; + +} + +#endif +#endif diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESO/fix_mvv_tdpd.cpp new file mode 100644 index 0000000000..382ce9033a --- /dev/null +++ b/src/USER-MESO/fix_mvv_tdpd.cpp @@ -0,0 +1,156 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This is a time integrator for position, velocity and concentration (x, + v and cc) using the modified velocity-Verlet (MVV) algorithm. + Setting verlet = 0.5 recovers the standard velocity-Verlet algorithm. + + Contributing author: Zhen Li (Brown University) + Email: zhen_li@brown.edu + + Please cite the related publication: + Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. "Transport + dissipative particle dynamics model for mesoscopic advection-diffusion + -reaction problems". The Journal of Chemical Physics, 2015, 143: 014101. +------------------------------------------------------------------------- */ + +#include +#include +#include "fix_mvv_tdpd.h" +#include "atom.h" +#include "force.h" +#include "update.h" +#include "respa.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixMvvTDPD::FixMvvTDPD(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (strcmp(style,"tdpd/verlet") != 0 && narg < 3) + error->all(FLERR,"Illegal fix mvv/tdpd command"); + + verlet = 0.5; + if(narg > 3) verlet = force->numeric(FLERR,arg[3]); + + cc_species = atom->cc_species; + + dynamic_group_allow = 1; + time_integrate = 1; +} + +/* ---------------------------------------------------------------------- */ + +int FixMvvTDPD::setmask() +{ + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= FINAL_INTEGRATE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixMvvTDPD::init() +{ + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; +} + +/* ---------------------------------------------------------------------- + allow for both per-type and per-atom mass +------------------------------------------------------------------------- */ + +void FixMvvTDPD::initial_integrate(int vflag) +{ + double dtfm; + // update v and x and cc of atoms in group + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double **cc = atom->cc; + double **cc_flux = atom->cc_flux; + double **vest = atom->vest; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (rmass) dtfm = dtf / rmass[i]; + else dtfm = dtf / mass[type[i]]; + + vest[i][0] = v[i][0] + dtfm * f[i][0]; + vest[i][1] = v[i][1] + dtfm * f[i][1]; + vest[i][2] = v[i][2] + dtfm * f[i][2]; + + x[i][0] += dtv * vest[i][0]; + x[i][1] += dtv * vest[i][1]; + x[i][2] += dtv * vest[i][2]; + v[i][0] += 2.0 * verlet * dtfm * f[i][0]; + v[i][1] += 2.0 * verlet * dtfm * f[i][1]; + v[i][2] += 2.0 * verlet * dtfm * f[i][2]; + for(int k = 0; k < cc_species; k++) + cc[i][k] += 0.5 * dtv * cc_flux[i][k]; + } +} + +/* ---------------------------------------------------------------------- */ + +void FixMvvTDPD::final_integrate() +{ + double dtfm; + + // update v of atoms in group + + double **v = atom->v; + double **f = atom->f; + double **cc = atom->cc; + double **cc_flux = atom->cc_flux; + double **vest = atom->vest; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (rmass) dtfm = dtf / rmass[i]; + else dtfm = dtf / mass[type[i]]; + + v[i][0] = vest[i][0] + dtfm * f[i][0]; + v[i][1] = vest[i][1] + dtfm * f[i][1]; + v[i][2] = vest[i][2] + dtfm * f[i][2]; + for(int k = 0; k < cc_species; k++) + cc[i][k] += 0.5 * dtv * cc_flux[i][k]; + } +} + +/* ---------------------------------------------------------------------- */ + +void FixMvvTDPD::reset_dt() +{ + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; +} diff --git a/src/USER-MESO/fix_mvv_tdpd.h b/src/USER-MESO/fix_mvv_tdpd.h new file mode 100644 index 0000000000..7adb23af69 --- /dev/null +++ b/src/USER-MESO/fix_mvv_tdpd.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(mvv/tdpd,FixMvvTDPD) + +#else + +#ifndef LMP_FIX_MVV_TDPD_H +#define LMP_FIX_MVV_TDPD_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixMvvTDPD : public Fix { + public: + FixMvvTDPD(class LAMMPS *, int, char **); + virtual ~FixMvvTDPD() {} + int setmask(); + virtual void init(); + virtual void initial_integrate(int); + virtual void final_integrate(); + virtual void reset_dt(); + + protected: + double dtv, dtf; + double verlet; + int cc_species; +}; + +} + +#endif +#endif diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESO/fix_tdpd_source.cpp new file mode 100644 index 0000000000..3dfeba4787 --- /dev/null +++ b/src/USER-MESO/fix_tdpd_source.cpp @@ -0,0 +1,120 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include "fix_tdpd_source.h" +#include "atom.h" +#include "comm.h" +#include "update.h" +#include "modify.h" +#include "domain.h" +#include "lattice.h" +#include "input.h" +#include "variable.h" +#include "error.h" +#include "force.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixTDPDSource::FixTDPDSource(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (strcmp(style,"tdpd/source") != 0 && narg < 4) + error->all(FLERR,"Illegal fix tdpd/source command"); + + int iarg = 3; + cc_index = force->inumeric(FLERR,arg[iarg++]); + + if (strcmp(arg[iarg],"sphere") == 0) option = 0; + else if (strcmp(arg[iarg],"cuboid") == 0) option = 1; + else error->all(FLERR,"Illegal fix tdpd/source command"); + iarg++; + + if(option == 0){ + if (narg != 10 ) error->all(FLERR,"Illegal fix tdpd/source command (5 args for sphere)"); + center[0] = force->numeric(FLERR,arg[iarg++]); + center[1] = force->numeric(FLERR,arg[iarg++]); + center[2] = force->numeric(FLERR,arg[iarg++]); + radius = force->numeric(FLERR,arg[iarg++]); + value = force->numeric(FLERR,arg[iarg++]); + } + else if(option == 1){ + if (narg != 12 ) error->all(FLERR,"Illegal fix tdpd/edpd command (7 args for cuboid)"); + center[0] = force->numeric(FLERR,arg[iarg++]); + center[1] = force->numeric(FLERR,arg[iarg++]); + center[2] = force->numeric(FLERR,arg[iarg++]); + dLx = force->numeric(FLERR,arg[iarg++]); + dLy = force->numeric(FLERR,arg[iarg++]); + dLz = force->numeric(FLERR,arg[iarg++]); + value = force->numeric(FLERR,arg[iarg++]); + } + else error->all(FLERR,"Illegal fix tdpd/source command"); +} + +/* ---------------------------------------------------------------------- */ + +FixTDPDSource::~FixTDPDSource() +{ +} + +/* ---------------------------------------------------------------------- */ + +int FixTDPDSource::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixTDPDSource::init() +{ +} + +/* ---------------------------------------------------------------------- */ + +void FixTDPDSource::post_force(int vflag) +{ + double **x = atom->x; + double **cc_flux = atom->cc_flux; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + double drx, dry, drz, rsq; + double radius_sq = radius*radius*radius; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + if(option == 0){ + drx = x[i][0] - center[0]; + dry = x[i][1] - center[1]; + drz = x[i][2] - center[2]; + rsq = drx*drx + dry*dry + drz*drz; + if(rsq < radius_sq) + cc_flux[i][cc_index-1] += value; + } + else if(option == 1){ + drx = x[i][0] - center[0]; + dry = x[i][1] - center[1]; + drz = x[i][2] - center[2]; + if(abs(drx) <= 0.5*dLx && abs(dry) <= 0.5*dLy && abs(drz) <= 0.5*dLz) + cc_flux[i][cc_index-1] += value; + } + } + } +} diff --git a/src/USER-MESO/fix_tdpd_source.h b/src/USER-MESO/fix_tdpd_source.h new file mode 100644 index 0000000000..302fe82090 --- /dev/null +++ b/src/USER-MESO/fix_tdpd_source.h @@ -0,0 +1,45 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(tdpd/source,FixTDPDSource) + +#else + +#ifndef LMP_FIX_TDPDSOURCE_H +#define LMP_FIX_TDPDSOURCE_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixTDPDSource : public Fix { + public: + FixTDPDSource(class LAMMPS *, int, char **); + ~FixTDPDSource(); + int setmask(); + void init(); + void post_force(int); + + protected: + int option; + int cc_index; + double center[3], radius, dLx, dLy, dLz; + double value; +}; + +} + +#endif +#endif diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp new file mode 100644 index 0000000000..c1c100db43 --- /dev/null +++ b/src/USER-MESO/pair_edpd.cpp @@ -0,0 +1,551 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Zhen Li (Brown University) + Email: zhen_li@brown.edu +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "pair_edpd.h" +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "update.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "random_mars.h" +#include "citeme.h" +#include "memory.h" +#include "error.h" +#include +#include + +using namespace LAMMPS_NS; + +#define MIN(A,B) ((A) < (B) ? (A) : (B)) +#define MAX(A,B) ((A) > (B) ? (A) : (B)) + +#define EPSILON 1.0e-10 + +static const char cite_pair_edpd[] = + "pair edpd command:\n\n" + "@Article{ZLi2014_JCP,\n" + " author = {Li, Z. and Tang, Y.-H. and Lei, H. and Caswell, B. and Karniadakis, G.E.},\n" + " title = {Energy-conserving dissipative particle dynamics with temperature-dependent properties},\n" + " journal = {Journal of Computational Physics},\n" + " year = {2014},\n" + " volume = {265},\n" + " pages = {113--127}\n" + "}\n\n" + "@Article{ZLi2015_CC,\n" + " author = {Li, Z. and Tang, Y.-H. and Li, X. and Karniadakis, G.E.},\n" + " title = {Mesoscale modeling of phase transition dynamics of thermoresponsive polymers},\n" + " journal = {Chemical Communications},\n" + " year = {2015},\n" + " volume = {51},\n" + " pages = {11038--11040}\n" + "}\n\n"; +; + +/* ---------------------------------------------------------------------- */ + +PairEDPD::PairEDPD(LAMMPS *lmp) : Pair(lmp) +{ + if (lmp->citeme) lmp->citeme->add(cite_pair_edpd); + writedata = 1; + random = NULL; + randomT = NULL; +} + +/* ---------------------------------------------------------------------- */ + +PairEDPD::~PairEDPD() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(cutT); + + memory->destroy(a0); + memory->destroy(gamma); + memory->destroy(power); + memory->destroy(kappa); + memory->destroy(powerT); + } + if (power_flag) memory->destroy(sc); + if (kappa_flag) memory->destroy(kc); + + if (random) delete random; + if (randomT) delete randomT; +} + +/* ---------------------------------------------------------------------- */ + +void PairEDPD::compute(int eflag, int vflag) +{ + double evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double *T = atom->edpd_temp; + double *Q = atom->edpd_flux; + double *cv = atom->edpd_cv; + int *type = atom->type; + double *mass = atom->mass; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double dtinvsqrt = 1.0/sqrt(update->dt); + double kboltz = 1.0; + + int inum = list->inum; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + for (int ii = 0; ii < inum; ii++) { + int i = ilist[ii]; + double xtmp = x[i][0]; + double ytmp = x[i][1]; + double ztmp = x[i][2]; + double vxtmp = v[i][0]; + double vytmp = v[i][1]; + double vztmp = v[i][2]; + int itype = type[i]; + int *jlist = firstneigh[i]; + int jnum = numneigh[i]; + + for (int jj = 0; jj < jnum; jj++) { + int j = jlist[jj]; + double factor_dpd = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + double delx = xtmp - x[j][0]; + double dely = ytmp - x[j][1]; + double delz = ztmp - x[j][2]; + double rsq = delx*delx + dely*dely + delz*delz; + int jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + double r = sqrt(rsq); + if (r < EPSILON) continue; + double rinv = 1.0/r; + double delvx = vxtmp - v[j][0]; + double delvy = vytmp - v[j][1]; + double delvz = vztmp - v[j][2]; + double dot = delx*delvx + dely*delvy + delz*delvz; + double vijeij = dot*rinv; + double randnum = random->gaussian(); + + double T_ij=0.5*(T[i]+T[j]); + double T_pow[4]; + T_pow[0] = T_ij - 1.0; + T_pow[1] = T_pow[0]*T_pow[0]; + T_pow[2] = T_pow[0]*T_pow[1]; + T_pow[3] = T_pow[0]*T_pow[2]; + + double power_d = power[itype][jtype]; + if(power_flag){ + double factor = 1.0; + for(int k = 0; k < 4; k++) + factor += sc[itype][jtype][k]*T_pow[k]; + power_d *= factor; + } + + power_d = MAX(0.01,power_d); + double wc = 1.0 - r/cut[itype][jtype]; + wc = MAX(0.0,MIN(1.0,wc)); + double wr = pow(wc, 0.5*power_d); + + double GammaIJ = gamma[itype][jtype]; + double SigmaIJ = 4.0*GammaIJ*kboltz*T[i]*T[j]/(T[i]+T[j]); + SigmaIJ = sqrt(SigmaIJ); + + double fpair = a0[itype][jtype]*T_ij*wc; + fpair -= GammaIJ *wr*wr *dot*rinv; + fpair += SigmaIJ * wr *randnum * dtinvsqrt; + fpair *= factor_dpd*rinv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + + // heat transfer + double dQc,dQd,dQr; + if( r < cutT[itype][jtype]) { + double wrT = 1.0 - r/cutT[itype][jtype]; + wrT = MAX(0.0,MIN(1.0,wrT)); + wrT = pow(wrT, 0.5*powerT[itype][jtype]); + double randnumT = randomT->gaussian(); + randnumT = MAX(-5.0,MIN(randnum,5.0)); + + double kappaT = kappa[itype][jtype]; + if(kappa_flag) { + double factor = 1.0; + for(int k = 0; k < 4; k++) + factor += kc[itype][jtype][k]*T_pow[k]; + kappaT *= factor; + } + + double kij = cv[i]*cv[j]*kappaT * T_ij*T_ij; + double alphaij = sqrt(2.0*kboltz*kij); + + dQc = kij * wrT*wrT * ( T[j] - T[i] )/(T[i]*T[j]); + dQd = wr*wr*( GammaIJ * vijeij*vijeij - SigmaIJ*SigmaIJ/mass[itype] ) - SigmaIJ * wr *vijeij *randnum; + dQd /= (cv[i]+cv[j]); + dQr = alphaij * wrT * dtinvsqrt * randnumT; + Q[i] += (dQc + dQd + dQr ); + } + //----------------------------------------------------------- + + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + Q[j] -= ( dQc - dQd + dQr ); + } + + if (eflag) { + evdwl = 0.5*a0[itype][jtype]*T_ij*cut[itype][jtype] * wc*wc; + evdwl *= factor_dpd; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairEDPD::allocate() +{ + int i,j; + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (i = 1; i <= n; i++) + for (j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(cutT,n+1,n+1,"pair:cutT"); + memory->create(a0,n+1,n+1,"pair:a0"); + memory->create(gamma,n+1,n+1,"pair:gamma"); + memory->create(power,n+1,n+1,"pair:power"); + memory->create(kappa,n+1,n+1,"pair:kappa"); + memory->create(powerT,n+1,n+1,"pair:powerT"); + +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairEDPD::settings(int narg, char **arg) +{ + if (narg != 2) error->all(FLERR,"Illegal pair_style command"); + + cut_global = force->numeric(FLERR,arg[0]); + seed = force->inumeric(FLERR,arg[1]); + + // initialize Marsaglia RNG with processor-unique seed + + if (seed <= 0 ) { + struct timespec time; + clock_gettime( CLOCK_REALTIME, &time ); + seed = time.tv_nsec; // if seed is non-positive, get the current time as the seed + } + delete random; + random = new RanMars(lmp,(seed + comm->me) % 900000000); + randomT = new RanMars(lmp,(2*seed + comm->me) % 900000000); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) + cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairEDPD::coeff(int narg, char **arg) +{ + if (narg < 9) + error->all(FLERR,"Incorrect args for pair edpd coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double a0_one = force->numeric(FLERR,arg[2]); + double gamma_one = force->numeric(FLERR,arg[3]); + double power_one = force->numeric(FLERR,arg[4]); + double cut_one = force->numeric(FLERR,arg[5]); + double kappa_one = force->numeric(FLERR,arg[6]); + double powerT_one= force->numeric(FLERR,arg[7]); + double cutT_one = force->numeric(FLERR,arg[8]); + + int iarg = 9; + power_flag = kappa_flag = 0; + double sc_one[4], kc_one[4]; + int n = atom->ntypes; + while (iarg < narg) { + if (strcmp(arg[iarg],"power") == 0) { + if (iarg+5 > narg) error->all(FLERR,"Illegal pair edpd coefficients"); + for (int i = 0; i < 4; i++) + sc_one[i] = force->numeric(FLERR,arg[iarg+i+1]); + iarg += 5; + power_flag = 1; + memory->create(sc,n+1,n+1,4,"pair:sc"); + } else if (strcmp(arg[iarg],"kappa") == 0) { + if (iarg+5 > narg) error->all(FLERR,"Illegal pair edpd coefficients"); + for (int i = 0; i < 4; i++) + kc_one[i] = force->numeric(FLERR,arg[iarg+i+1]); + iarg += 5; + kappa_flag = 1; + memory->create(kc,n+1,n+1,4,"pair:kc"); + } else error->all(FLERR,"Illegal pair edpd coefficients"); + } + + int count = 0; + for (int i = ilo; i <= ihi; i++) + for (int j = MAX(jlo,i); j <= jhi; j++) { + a0[i][j] = a0_one; + gamma[i][j] = gamma_one; + power[i][j] = power_one; + cut[i][j] = cut_one; + kappa[i][j] = kappa_one; + powerT[i][j]= powerT_one; + cutT[i][j] = cutT_one; + + if(power_flag) + for (int k = 0; k < 4; k++) + sc[i][j][k] = sc_one[k]; + + if(kappa_flag) + for (int k = 0; k < 4; k++) + kc[i][j][k] = kc_one[k]; + + setflag[i][j] = 1; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairEDPD::init_style() +{ + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair edpd requires ghost atoms store velocity"); + + // if newton off, forces between atoms ij will be double computed + // using different random numbers + + if (force->newton_pair == 0 && comm->me == 0) error->warning(FLERR, + "Pair tdpd needs newton pair on for momentum conservation"); + + neighbor->request(this,instance_me); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairEDPD::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + cut[j][i] = cut[i][j]; + cutT[j][i] = cutT[i][j]; + a0[j][i] = a0[i][j]; + gamma[j][i] = gamma[i][j]; + power[j][i] = power[i][j]; + kappa[j][i] = kappa[i][j]; + powerT[j][i]= powerT[i][j]; + + if(power_flag) + for (int k = 0; k < 4; k++) + sc[j][i][k] = sc[i][j][k]; + + if(kappa_flag) + for (int k = 0; k < 4; k++) + kc[j][i][k] = kc[i][j][k]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairEDPD::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&a0[i][j],sizeof(double),1,fp); + fwrite(&gamma[i][j],sizeof(double),1,fp); + fwrite(&power[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + fwrite(&kappa[i][j],sizeof(double),1,fp); + fwrite(&powerT[i][j],sizeof(double),1,fp); + fwrite(&cutT[i][j],sizeof(double),1,fp); + if(power_flag) + for (int k = 0; k < 4; k++) + fwrite(&sc[i][j][k],sizeof(double),1,fp); + + if(kappa_flag) + for (int k = 0; k < 4; k++) + fwrite(&kc[i][j][k],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairEDPD::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int me = comm->me; + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&a0[i][j],sizeof(double),1,fp); + fread(&gamma[i][j],sizeof(double),1,fp); + fread(&power[i][j],sizeof(double),1,fp); + fread(&cut[i][j],sizeof(double),1,fp); + fread(&kappa[i][j],sizeof(double),1,fp); + fread(&powerT[i][j],sizeof(double),1,fp); + fread(&cutT[i][j],sizeof(double),1,fp); + if(power_flag) + for (int k = 0; k < 4; k++) + fread(&sc[i][j][k],sizeof(double),1,fp); + + if(kappa_flag) + for (int k = 0; k < 4; k++) + fread(&kc[i][j][k],sizeof(double),1,fp); + } + MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&power[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&kappa[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&powerT[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cutT[i][j],1,MPI_DOUBLE,0,world); + if(power_flag) + for (int k = 0; k < 4; k++) + MPI_Bcast(&sc[i][j][k],1,MPI_DOUBLE,0,world); + + if(kappa_flag) + for (int k = 0; k < 4; k++) + MPI_Bcast(&kc[i][j][k],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairEDPD::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&seed,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairEDPD::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_global,sizeof(double),1,fp); + fread(&seed,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&seed,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + + // initialize Marsaglia RNG with processor-unique seed + // same seed that pair_style command initially specified + + if (random) delete random; + random = new RanMars(lmp,seed + comm->me); + if (randomT) delete randomT; + randomT = new RanMars(lmp,seed + comm->me); +} + +/* ---------------------------------------------------------------------- */ + +double PairEDPD::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_dpd, double &fforce) +{ + double r,rinv,wc,phi; + double *T = atom->edpd_temp; + + r = sqrt(rsq); + if (r < EPSILON) { + fforce = 0.0; + return 0.0; + } + double T_ij = 0.5*(T[i]+T[j]); + rinv = 1.0/r; + wc = 1.0 - r/cut[itype][jtype]; + fforce = a0[itype][jtype]*T_ij*wc*factor_dpd*rinv; + + phi = 0.5*a0[itype][jtype]*T_ij*cut[itype][jtype]*wc*wc; + return factor_dpd*phi; +} diff --git a/src/USER-MESO/pair_edpd.h b/src/USER-MESO/pair_edpd.h new file mode 100644 index 0000000000..9ab0ad9670 --- /dev/null +++ b/src/USER-MESO/pair_edpd.h @@ -0,0 +1,85 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(edpd,PairEDPD) + +#else + +#ifndef LMP_PAIR_EDPD_H +#define LMP_PAIR_EDPD_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairEDPD : public Pair { + public: + PairEDPD(class LAMMPS *); + virtual ~PairEDPD(); + virtual void compute(int, int); + virtual void settings(int, char **); + virtual void coeff(int, char **); + void init_style(); + double init_one(int, int); + virtual void write_restart(FILE *); + virtual void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + double single(int, int, int, int, double, double, double, double &); + + protected: + double cut_global; + int seed; + double **cut,**cutT; + double **a0,**gamma; + double **power; + double **slope; + double **kappa; + double **powerT; + int power_flag, kappa_flag; + double ***sc,***kc; + class RanMars *random; + class RanMars *randomT; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +W: Pair tdpd needs newton pair on for momentum conservation + +Self-explanatory. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +*/ diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESO/pair_mdpd.cpp new file mode 100644 index 0000000000..bf78ea5af7 --- /dev/null +++ b/src/USER-MESO/pair_mdpd.cpp @@ -0,0 +1,425 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Zhen Li (Brown University) + Email: zhen_li@brown.edu +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "pair_mdpd.h" +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "update.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "random_mars.h" +#include "citeme.h" +#include "memory.h" +#include "error.h" +#include + +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-10 + +static const char cite_pair_mdpd[] = + "pair mdpd command:\n\n" + "@Article{ZLi2013_POF,\n" + " author = {Li, Z. and Hu, G.H. and Wang, Z.L. and Ma Y.B. and Zhou, Z.W.},\n" + " title = {Three dimensional flow structures in a moving droplet on substrate: a dissipative particle dynamics study},\n" + " journal = {Physics of Fluids},\n" + " year = {2013},\n" + " volume = {25},\n" + " pages = {072103}\n" + "}\n\n"; + +/* ---------------------------------------------------------------------- */ + +PairMDPD::PairMDPD(LAMMPS *lmp) : Pair(lmp) +{ + if (lmp->citeme) lmp->citeme->add(cite_pair_mdpd); + + writedata = 1; + random = NULL; +} + +/* ---------------------------------------------------------------------- */ + +PairMDPD::~PairMDPD() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(cut_r); + memory->destroy(A_att); + memory->destroy(B_rep); + memory->destroy(gamma); + memory->destroy(sigma); + } + if (random) delete random; +} + +/* ---------------------------------------------------------------------- */ + +void PairMDPD::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double vxtmp,vytmp,vztmp,delvx,delvy,delvz; + double rsq,r,rinv,dot,wc,wc_r, wr,randnum,factor_dpd; + int *ilist,*jlist,*numneigh,**firstneigh; + double rhoi, rhoj; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double *rho= atom->rho; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double dtinvsqrt = 1.0/sqrt(update->dt); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + vxtmp = v[i][0]; + vytmp = v[i][1]; + vztmp = v[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + rhoi = rho[i]; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_dpd = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + if (r < EPSILON) continue; // r can be 0.0 in MDPD systems + rinv = 1.0/r; + delvx = vxtmp - v[j][0]; + delvy = vytmp - v[j][1]; + delvz = vztmp - v[j][2]; + dot = delx*delvx + dely*delvy + delz*delvz; + + wc = 1.0 - r/cut[itype][jtype]; + wc_r = 1.0 - r/cut_r[itype][jtype]; + wc_r = MAX(wc_r,0.0); + wr = wc; + + rhoj = rho[j]; + randnum = random->gaussian(); + + // conservative force = A_att * wc + B_rep*(rhoi+rhoj)*wc_r + // drag force = -gamma * wr^2 * (delx dot delv) / r + // random force = sigma * wr * rnd * dtinvsqrt; + + fpair = A_att[itype][jtype]*wc + B_rep[itype][jtype]*(rhoi+rhoj)*wc_r; + fpair -= gamma[itype][jtype]*wr*wr*dot*rinv; + fpair += sigma[itype][jtype]*wr*randnum*dtinvsqrt; + fpair *= factor_dpd*rinv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + // unshifted eng of conservative term: + // eng shifted to 0.0 at cutoff + evdwl = 0.5*A_att[itype][jtype]*cut[itype][jtype] * wr*wr + 0.5*B_rep[itype][jtype]*cut_r[itype][jtype]*(rhoi+rhoj)*wc_r*wc_r; + evdwl *= factor_dpd; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz); + } + } + } + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairMDPD::allocate() +{ + int i,j; + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (i = 1; i <= n; i++) + for (j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(cut_r,n+1,n+1,"pair:cut_r"); + memory->create(A_att,n+1,n+1,"pair:A_att"); + memory->create(B_rep,n+1,n+1,"pair:B_rep"); + memory->create(gamma,n+1,n+1,"pair:gamma"); + memory->create(sigma,n+1,n+1,"pair:sigma"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairMDPD::settings(int narg, char **arg) +{ + if (narg != 3) error->all(FLERR,"Illegal pair_style command"); + + temperature = force->numeric(FLERR,arg[0]); + cut_global = force->numeric(FLERR,arg[1]); + seed = force->inumeric(FLERR,arg[2]); + + // initialize Marsaglia RNG with processor-unique seed + + if (seed <= 0 ) { + struct timespec time; + clock_gettime( CLOCK_REALTIME, &time ); + seed = time.tv_nsec; // if seed is non-positive, get the current time as the seed + } + delete random; + random = new RanMars(lmp,(seed + comm->me) % 900000000); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairMDPD::coeff(int narg, char **arg) +{ + if(narg != 7 ) error->all(FLERR,"Incorrect args for pair coefficients\n itype jtype A B gamma cutA cutB"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double A_one = force->numeric(FLERR,arg[2]); + double B_one = force->numeric(FLERR,arg[3]); + double gamma_one = force->numeric(FLERR,arg[4]); + double cut_one = force->numeric(FLERR,arg[5]); + double cut_two = force->numeric(FLERR,arg[6]); + + if(cut_one < cut_two) error->all(FLERR,"Incorrect args for pair coefficients\n cutA should be larger than cutB."); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + A_att[i][j] = A_one; + B_rep[i][j] = B_one; + gamma[i][j] = gamma_one; + cut[i][j] = cut_one; + cut_r[i][j] = cut_two; + setflag[i][j] = 1; + count++; + } + } + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairMDPD::init_style() +{ + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair mdpd requires ghost atoms store velocity"); + + // if newton off, forces between atoms ij will be double computed + // using different random numbers + + if (force->newton_pair == 0 && comm->me == 0) error->warning(FLERR, + "Pair mdpd needs newton pair on for momentum conservation"); + + neighbor->request(this,instance_me); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairMDPD::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + sigma[i][j] = sqrt(2.0*force->boltz*temperature*gamma[i][j]); + + cut[j][i] = cut[i][j]; + cut_r[j][i] = cut_r[i][j]; + A_att[j][i] = A_att[i][j]; + B_rep[j][i] = B_rep[i][j]; + gamma[j][i] = gamma[i][j]; + sigma[j][i] = sigma[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairMDPD::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&A_att[i][j],sizeof(double),1,fp); + fwrite(&B_rep[i][j],sizeof(double),1,fp); + fwrite(&gamma[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + fwrite(&cut_r[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairMDPD::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&A_att[i][j],sizeof(double),1,fp); + fread(&B_rep[i][j],sizeof(double),1,fp); + fread(&gamma[i][j],sizeof(double),1,fp); + fread(&cut[i][j],sizeof(double),1,fp); + fread(&cut_r[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&A_att[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&B_rep[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_r[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairMDPD::write_restart_settings(FILE *fp) +{ + fwrite(&temperature,sizeof(double),1,fp); + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&seed,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairMDPD::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&temperature,sizeof(double),1,fp); + fread(&cut_global,sizeof(double),1,fp); + fread(&seed,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&seed,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + + // initialize Marsaglia RNG with processor-unique seed + // same seed that pair_style command initially specified + + if (random) delete random; + random = new RanMars(lmp,seed + comm->me); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairMDPD::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g\n",i,A_att[i][i],B_rep[i][i],gamma[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairMDPD::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g %g %g\n",i,j,A_att[i][j],B_rep[i][j],gamma[i][j],cut[i][j],cut_r[i][j]); +} + diff --git a/src/USER-MESO/pair_mdpd.h b/src/USER-MESO/pair_mdpd.h new file mode 100644 index 0000000000..ea0389c7fe --- /dev/null +++ b/src/USER-MESO/pair_mdpd.h @@ -0,0 +1,84 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(mdpd,PairMDPD) + +#else + +#ifndef LMP_PAIR_MDPD_H +#define LMP_PAIR_MDPD_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairMDPD : public Pair { + public: + PairMDPD(class LAMMPS *); + virtual ~PairMDPD(); + virtual void compute(int, int); + virtual void settings(int, char **); + virtual void coeff(int, char **); + void init_style(); + double init_one(int, int); + virtual void write_restart(FILE *); + virtual void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + virtual void write_data(FILE *); + virtual void write_data_all(FILE *); + + protected: + double cut_global,temperature; + int seed; + double **cut, **cut_r; + double **A_att,**B_rep; + double **gamma,**sigma; + class RanMars *random; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair dpd requires ghost atoms store velocity + +Use the comm_modify vel yes command to enable this. + +W: Pair dpd needs newton pair on for momentum conservation + +Self-explanatory. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +*/ diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp new file mode 100644 index 0000000000..9c4d6f804f --- /dev/null +++ b/src/USER-MESO/pair_mdpd_rhosum.cpp @@ -0,0 +1,267 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ------------------------------------------------------------------------- */ + +/*----------------------------------------------------------------------- + This is a Child Class PairMDPD for taking care of density summation + before the force calculation. + The code uses 3D Lucy kernel, it can be modified for other kernels. + + Contributing author: Zhen Li (Brown University) +------------------------------------------------------------------------- */ + +#include +#include +#include "pair_mdpd_rhosum.h" +#include "atom.h" +#include "force.h" +#include "comm.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "memory.h" +#include "error.h" +#include "neighbor.h" +#include "update.h" +#include "domain.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairMDPDRhoSum::PairMDPDRhoSum(LAMMPS *lmp) : Pair(lmp) +{ + restartinfo = 0; + + // set comm size needed by this Pair + + comm_forward = 1; + first = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairMDPDRhoSum::~PairMDPDRhoSum() { + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + } +} + +/* ---------------------------------------------------------------------- + init specific to this pair style + ------------------------------------------------------------------------- */ + +void PairMDPDRhoSum::init_style() { + // need a full neighbor list + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; +} + +/* ---------------------------------------------------------------------- */ + +void PairMDPDRhoSum::compute(int eflag, int vflag) { + int i, j, ii, jj, jnum, itype, jtype; + double xtmp, ytmp, ztmp, delx, dely, delz; + double r, rsq, h, ih, ihsq; + int *jlist; + double wf; + // neighbor list variables + int inum, *ilist, *numneigh, **firstneigh; + + if (eflag || vflag) + ev_setup(eflag, vflag); + else + evflag = vflag_fdotr = 0; + + double **x = atom->x; + double *rho = atom->rho; + int *type = atom->type; + double *mass = atom->mass; + + // check consistency of pair coefficients + if (first) { + for (i = 1; i <= atom->ntypes; i++) + for (j = 1; i <= atom->ntypes; i++) + if (cutsq[i][j] > 0.0) + if (!setflag[i][i] || !setflag[j][j]) + if (comm->me == 0) + printf("mDPD particle types %d and %d interact, but not all of their single particle properties are set.\n", i, j); + + first = 0; + } + + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // recompute density + // we use a full neighborlist here + + // initialize density with zero self-contribution, + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + + h = cut[itype][itype]; + // Lucy kernel, 3d + wf = 2.0889086280811262819e0 / (h * h * h); + rho[i] = 0; + } + + // add density at each atom via kernel function overlap + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + jtype = type[j]; + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + + if (rsq < cutsq[itype][jtype]) { + h = cut[itype][jtype]; + ih = 1.0 / h; + ihsq = ih * ih; + + // Lucy kernel, 3d + r = sqrt(rsq); + wf = (h - r) * ihsq; + wf = 2.0889086280811262819e0 * (h + 3. * r) * wf * wf * wf * ih; + rho[i] += mass[jtype]*wf; + } + } + } + + // communicate densities + comm->forward_comm_pair(this); +} + +/* ---------------------------------------------------------------------- + allocate all arrays + ------------------------------------------------------------------------- */ + +void PairMDPDRhoSum::allocate() { + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); + + memory->create(cut, n + 1, n + 1, "pair:cut"); +} + +/* ---------------------------------------------------------------------- + global settings + ------------------------------------------------------------------------- */ + +void PairMDPDRhoSum::settings(int narg, char **arg) { + if (narg != 0) + error->all(FLERR,"Illegal number of setting arguments for pair_style mdpd/rhosum"); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs + ------------------------------------------------------------------------- */ + +void PairMDPDRhoSum::coeff(int narg, char **arg) { + if (narg != 3) + error->all(FLERR,"Incorrect number of args for mdpd/rhosum coefficients"); + if (!allocated) + allocate(); + + int ilo, ihi, jlo, jhi; + force->bounds(FLERR,arg[0], atom->ntypes, ilo, ihi); + force->bounds(FLERR,arg[1], atom->ntypes, jlo, jhi); + + double cut_one = force->numeric(FLERR,arg[2]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) + error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i + ------------------------------------------------------------------------- */ + +double PairMDPDRhoSum::init_one(int i, int j) { + if (setflag[i][j] == 0) { + error->all(FLERR,"All pair mdpd/rhosum coeffs are not set"); + } + + cut[j][i] = cut[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- */ + +double PairMDPDRhoSum::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_lj, double &fforce) { + fforce = 0.0; + + return 0.0; +} + +/* ---------------------------------------------------------------------- */ + +int PairMDPDRhoSum::pack_forward_comm(int n, int *list, double *buf, + int pbc_flag, int *pbc) { + int i, j, m; + double *rho = atom->rho; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = rho[j]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void PairMDPDRhoSum::unpack_forward_comm(int n, int first, double *buf) { + int i, m, last; + double *rho = atom->rho; + + m = 0; + last = first + n; + for (i = first; i < last; i++) + rho[i] = buf[m++]; +} diff --git a/src/USER-MESO/pair_mdpd_rhosum.h b/src/USER-MESO/pair_mdpd_rhosum.h new file mode 100644 index 0000000000..a972ec7ccf --- /dev/null +++ b/src/USER-MESO/pair_mdpd_rhosum.h @@ -0,0 +1,50 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(mdpd/rhosum,PairMDPDRhoSum) + +#else + +#ifndef LMP_PAIR_MDPD_RHOSUM_H +#define LMP_PAIR_MDPD_RHOSUM_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairMDPDRhoSum : public Pair { + public: + PairMDPDRhoSum(class LAMMPS *); + virtual ~PairMDPDRhoSum(); + void init_style(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + virtual double init_one(int, int); + virtual double single(int, int, int, int, double, double, double, double &); + int pack_forward_comm(int, int *, double *, int, int *); + void unpack_forward_comm(int, int, double *); + + protected: + double **cut; + int first; + + void allocate(); +}; + +} + +#endif +#endif diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp new file mode 100644 index 0000000000..22c856ee3f --- /dev/null +++ b/src/USER-MESO/pair_tdpd.cpp @@ -0,0 +1,477 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Zhen Li (Brown University) + Email: zhen_li@brown.edu +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "pair_tdpd.h" +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "update.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "random_mars.h" +#include "citeme.h" +#include "memory.h" +#include "error.h" +#include + +using namespace LAMMPS_NS; + +#define MIN(A,B) ((A) < (B) ? (A) : (B)) +#define MAX(A,B) ((A) > (B) ? (A) : (B)) + +#define EPSILON 1.0e-10 + +static const char cite_pair_tdpd[] = + "pair tdpd command:\n\n" + "@Article{ZLi2015_JCP,\n" + " author = {Li, Z. and Yazdani, A. and Tartakovsky, A. and Karniadakis, G.E.},\n" + " title = {Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems},\n" + " journal = {The Journal of Chemical Physics},\n" + " year = {2015},\n" + " volume = {143},\n" + " pages = {014101}\n" + "}\n\n"; + +/* ---------------------------------------------------------------------- */ + +PairTDPD::PairTDPD(LAMMPS *lmp) : Pair(lmp) +{ + if (lmp->citeme) lmp->citeme->add(cite_pair_tdpd); + cc_species = atom->cc_species; + + writedata = 1; + random = NULL; +} + +/* ---------------------------------------------------------------------- */ + +PairTDPD::~PairTDPD() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(cutcc); + + memory->destroy(a0); + memory->destroy(gamma); + memory->destroy(sigma); + + memory->destroy(power); + memory->destroy(kappa); + memory->destroy(epsilon); + memory->destroy(powercc); + } + + if (random) delete random; +} + +/* ---------------------------------------------------------------------- */ + +void PairTDPD::compute(int eflag, int vflag) +{ + double evdwl = 0.0; + double fpair; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double **cc = atom->cc; + double **cc_flux = atom->cc_flux; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double dtinvsqrt = 1.0/sqrt(update->dt); + + int inum = list->inum; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + for (int ii = 0; ii < inum; ii++) { + int i = ilist[ii]; + double xtmp = x[i][0]; + double ytmp = x[i][1]; + double ztmp = x[i][2]; + double vxtmp = v[i][0]; + double vytmp = v[i][1]; + double vztmp = v[i][2]; + int itype = type[i]; + int *jlist = firstneigh[i]; + int jnum = numneigh[i]; + + for (int jj = 0; jj < jnum; jj++) { + int j = jlist[jj]; + double factor_dpd = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + double delx = xtmp - x[j][0]; + double dely = ytmp - x[j][1]; + double delz = ztmp - x[j][2]; + double rsq = delx*delx + dely*dely + delz*delz; + int jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + double r = sqrt(rsq); + if (r < EPSILON) continue; // r can be 0.0 in DPD systems + double rinv = 1.0/r; + double delvx = vxtmp - v[j][0]; + double delvy = vytmp - v[j][1]; + double delvz = vztmp - v[j][2]; + double dot = delx*delvx + dely*delvy + delz*delvz; + double wc = 1.0 - r/cut[itype][jtype]; + wc = MAX(0,MIN(1.0,wc)); + double wr = pow(wc, 0.5*power[itype][jtype]); + double randnum = random->gaussian(); + + // conservative force = a0 * wc + // drag force = -gamma * wr^2 * (delx dot delv) / r + // random force = sigma * wr^(power/2) * rnd * dtinvsqrt; + + double fpair = a0[itype][jtype]*wc; + fpair -= gamma[itype][jtype]*wr*wr*dot*rinv; + fpair += sigma[itype][jtype]*wr*randnum*dtinvsqrt; + fpair *= factor_dpd*rinv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + + // chemical concentration transport + if( r < cutcc[itype][jtype]) { + for(int k=0; kgaussian(); + randnum = MAX(-5.0,MIN(randnum,5.0)); + double dQc = -kappa[itype][jtype][k] * wcr*wcr *(cc[i][k]-cc[j][k]); + double dQr = epsilon[itype][jtype][k] *wcr* (cc[i][k]+cc[j][k]) *randnum*dtinvsqrt; + cc_flux[i][k] += (dQc + dQr); + if (newton_pair || j < nlocal) + cc_flux[j][k] -= ( dQc + dQr ); + } + } + //----------------------------------------------------------- + + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wc*wc; + evdwl *= factor_dpd; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairTDPD::allocate() +{ + int i,j; + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (i = 1; i <= n; i++) + for (j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(cutcc,n+1,n+1,"pair:cutcc"); + memory->create(a0,n+1,n+1,"pair:a0"); + memory->create(gamma,n+1,n+1,"pair:gamma"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + memory->create(power,n+1,n+1,"pair:power"); + memory->create(kappa,n+1,n+1,cc_species,"pair:kappa"); + memory->create(epsilon,n+1,n+1,cc_species,"pair:epsilon"); + memory->create(powercc,n+1,n+1,cc_species,"pair:powercc"); + + for (i = 0; i <= atom->ntypes; i++) + for (j = 0; j <= atom->ntypes; j++) + sigma[i][j] = gamma[i][j] = 0.0; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairTDPD::settings(int narg, char **arg) +{ + if (narg != 3) error->all(FLERR,"Illegal pair_style command"); + + temperature = force->numeric(FLERR,arg[0]); + cut_global = force->numeric(FLERR,arg[1]); + seed = force->inumeric(FLERR,arg[2]); + + // initialize Marsaglia RNG with processor-unique seed + + if (seed <= 0 ) { + struct timespec time; + clock_gettime( CLOCK_REALTIME, &time ); + seed = time.tv_nsec; // if seed is non-positive, get the current time as the seed + } + delete random; + random = new RanMars(lmp,(seed + comm->me) % 900000000); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) + cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairTDPD::coeff(int narg, char **arg) +{ + if (narg != 7 + 3*cc_species) + error->all(FLERR,"Incorrect args for pair tdpd coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double a0_one = force->numeric(FLERR,arg[2]); + double gamma_one = force->numeric(FLERR,arg[3]); + double power_one = force->numeric(FLERR,arg[4]); + double cut_one = force->numeric(FLERR,arg[5]); + double cutcc_one = force->numeric(FLERR,arg[6]); + double kappa_one[cc_species],epsilon_one[cc_species],powercc_one[cc_species]; + for(int k=0; knumeric(FLERR,arg[7+3*k]); + epsilon_one[k] = force->numeric(FLERR,arg[8+3*k]); + powercc_one[k] = force->numeric(FLERR,arg[9+3*k]); + } + + int count = 0; + for (int i = ilo; i <= ihi; i++) + for (int j = MAX(jlo,i); j <= jhi; j++) { + a0[i][j] = a0_one; + gamma[i][j] = gamma_one; + power[i][j] = power_one; + cut[i][j] = cut_one; + cutcc[i][j] = cutcc_one; + for(int k=0; kall(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairTDPD::init_style() +{ + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair tdpd requires ghost atoms store velocity"); + + // if newton off, forces between atoms ij will be double computed + // using different random numbers + + if (force->newton_pair == 0 && comm->me == 0) error->warning(FLERR, + "Pair tdpd needs newton pair on for momentum conservation"); + + neighbor->request(this,instance_me); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairTDPD::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + sigma[i][j] = sqrt(2.0*force->boltz*temperature*gamma[i][j]); + + cut[j][i] = cut[i][j]; + cutcc[j][i] = cutcc[i][j]; + a0[j][i] = a0[i][j]; + gamma[j][i] = gamma[i][j]; + sigma[j][i] = sigma[i][j]; + power[j][i] = power[i][j]; + for(int k=0; kntypes; i++) + for (int j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&a0[i][j],sizeof(double),1,fp); + fwrite(&gamma[i][j],sizeof(double),1,fp); + fwrite(&power[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + fwrite(&cutcc[i][j],sizeof(double),1,fp); + for(int k=0; kme; + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&a0[i][j],sizeof(double),1,fp); + fread(&gamma[i][j],sizeof(double),1,fp); + fread(&power[i][j],sizeof(double),1,fp); + fread(&cut[i][j],sizeof(double),1,fp); + fread(&cutcc[i][j],sizeof(double),1,fp); + for(int k=0; kme == 0) { + fread(&temperature,sizeof(double),1,fp); + fread(&cut_global,sizeof(double),1,fp); + fread(&seed,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&seed,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + + // initialize Marsaglia RNG with processor-unique seed + // same seed that pair_style command initially specified + + if (random) delete random; + random = new RanMars(lmp,seed + comm->me); +} + +/* ---------------------------------------------------------------------- */ + +double PairTDPD::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_dpd, double &fforce) +{ + double r,rinv,wc,phi; + + r = sqrt(rsq); + if (r < EPSILON) { + fforce = 0.0; + return 0.0; + } + + rinv = 1.0/r; + wc = 1.0 - r/cut[itype][jtype]; + fforce = a0[itype][jtype]*wc*factor_dpd*rinv; + + phi = 0.5*a0[itype][jtype]*cut[itype][jtype]*wc*wc; + return factor_dpd*phi; +} diff --git a/src/USER-MESO/pair_tdpd.h b/src/USER-MESO/pair_tdpd.h new file mode 100644 index 0000000000..9245308d38 --- /dev/null +++ b/src/USER-MESO/pair_tdpd.h @@ -0,0 +1,81 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(tdpd,PairTDPD) + +#else + +#ifndef LMP_PAIR_TDPD_H +#define LMP_PAIR_TDPD_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairTDPD : public Pair { + public: + PairTDPD(class LAMMPS *); + virtual ~PairTDPD(); + virtual void compute(int, int); + virtual void settings(int, char **); + virtual void coeff(int, char **); + void init_style(); + double init_one(int, int); + virtual void write_restart(FILE *); + virtual void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + double single(int, int, int, int, double, double, double, double &); + + protected: + double cut_global,temperature; + int seed,cc_species; + double **cut,**cutcc; + double **a0,**gamma,**sigma; + double **power; + double ***kappa,***epsilon; + double ***powercc; + class RanMars *random; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +W: Pair tdpd needs newton pair on for momentum conservation + +Self-explanatory. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +*/ diff --git a/src/atom.cpp b/src/atom.cpp index e46b1a7242..d4c00bc0a5 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -105,6 +105,11 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) dpdTheta = NULL; ssaAIR = NULL; + // USER-MESO + + cc = cc_flux = NULL; + edpd_temp = edpd_flux = edpd_cv = NULL; + // USER-SMD contact_radius = NULL; @@ -169,7 +174,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) cs_flag = csforce_flag = vforce_flag = etag_flag = 0; rho_flag = e_flag = cv_flag = vest_flag = 0; - dpd_flag = 0; + dpd_flag = edpd_flag = tdpd_flag = 0; // USER-SMD @@ -302,6 +307,12 @@ Atom::~Atom() memory->destroy(duChem); memory->destroy(ssaAIR); + memory->destroy(cc); + memory->destroy(cc_flux); + memory->destroy(edpd_temp); + memory->destroy(edpd_flux); + memory->destroy(edpd_cv); + memory->destroy(nspecial); memory->destroy(special); @@ -2194,6 +2205,7 @@ void *Atom::extract(char *name) if (strcmp(name, "damage") == 0) return (void *) damage; if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta; + if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp; return NULL; } diff --git a/src/atom.h b/src/atom.h index 0f84c8242f..29a1c5d69e 100644 --- a/src/atom.h +++ b/src/atom.h @@ -95,6 +95,13 @@ class Atom : protected Pointers { int nspecies_dpd; int *ssaAIR; // Shardlow Splitting Algorithm Active Interaction Region number + // USER-MESO package + + double **cc, **cc_flux; // cc = chemical concentration + double *edpd_temp,*edpd_flux; // temperature and heat flux + double *edpd_cv; // heat capacity + int cc_species; + // molecular info int **nspecial; // 0,1,2 = cumulative # of 1-2,1-3,1-4 neighs @@ -138,7 +145,7 @@ class Atom : protected Pointers { int vfrac_flag,spin_flag,eradius_flag,ervel_flag,erforce_flag; int cs_flag,csforce_flag,vforce_flag,ervelforce_flag,etag_flag; int rho_flag,e_flag,cv_flag,vest_flag; - int dpd_flag; + int dpd_flag,edpd_flag,tdpd_flag; // USER-SMD package diff --git a/src/set.cpp b/src/set.cpp index 59625b7e6c..2b1c0edee2 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -41,11 +41,12 @@ using namespace LAMMPS_NS; using namespace MathConst; enum{ATOM_SELECT,MOL_SELECT,TYPE_SELECT,GROUP_SELECT,REGION_SELECT}; + enum{TYPE,TYPE_FRACTION,MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,LENGTH,TRI, DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,THETA,THETA_RANDOM,ANGMOM,OMEGA, DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER, - MESO_E,MESO_CV,MESO_RHO,SMD_MASS_DENSITY,SMD_CONTACT_RADIUS,DPDTHETA, - INAME,DNAME}; + MESO_E,MESO_CV,MESO_RHO,EDPD_TEMP,EDPD_CV,CC,SMD_MASS_DENSITY, + SMD_CONTACT_RADIUS,DPDTHETA,INAME,DNAME}; #define BIG INT_MAX @@ -419,6 +420,46 @@ void Set::command(int narg, char **arg) set(MESO_RHO); iarg += 2; + } else if (strcmp(arg[iarg],"edpd/temp") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); + if (strcmp(arg[iarg+1],"NULL") == 0) dvalue = -1.0; + else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else { + dvalue = force->numeric(FLERR,arg[iarg+1]); + if (dvalue < 0.0) error->all(FLERR,"Illegal set command"); + } + if (!atom->edpd_flag) + error->all(FLERR,"Cannot set edpd/temp for this atom style"); + set(EDPD_TEMP); + iarg += 2; + + } else if (strcmp(arg[iarg],"edpd/cv") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); + if (strcmp(arg[iarg+1],"NULL") == 0) dvalue = -1.0; + else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else { + dvalue = force->numeric(FLERR,arg[iarg+1]); + if (dvalue < 0.0) error->all(FLERR,"Illegal set command"); + } + if (!atom->edpd_flag) + error->all(FLERR,"Cannot set edpd/cv for this atom style"); + set(EDPD_CV); + iarg += 2; + + } else if (strcmp(arg[iarg],"cc") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal set command"); + if (strcmp(arg[iarg+1],"NULL") == 0) dvalue = -1.0; + else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else { + cc_index = force->inumeric(FLERR,arg[iarg+1]); + dvalue = force->numeric(FLERR,arg[iarg+2]); + if (cc_index < 1) error->all(FLERR,"Illegal set command"); + } + if (!atom->tdpd_flag) + error->all(FLERR,"Cannot set cc for this atom style"); + set(CC); + iarg += 3; + } else if (strcmp(arg[iarg],"smd/mass/density") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); @@ -476,14 +517,28 @@ void Set::command(int narg, char **arg) } else error->all(FLERR,"Illegal set command"); // statistics + // for CC option, include species index MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world); if (comm->me == 0) { - if (screen) fprintf(screen," %d settings made for %s\n", - allcount,arg[origarg]); - if (logfile) fprintf(logfile," %d settings made for %s\n", - allcount,arg[origarg]); + + if (screen) { + if (strcmp(arg[origarg],"cc") == 0) + fprintf(screen," %d settings made for %s index %s\n", + allcount,arg[origarg],arg[origarg+1]); + else + fprintf(screen," %d settings made for %s\n", + allcount,arg[origarg]); + } + if (logfile) { + if (strcmp(arg[origarg],"cc") == 0) + fprintf(logfile," %d settings made for %s index %s\n", + allcount,arg[origarg],arg[origarg+1]); + else + fprintf(logfile," %d settings made for %s\n", + allcount,arg[origarg]); + } } } @@ -663,6 +718,11 @@ void Set::set(int keyword) else if (keyword == MESO_E) atom->e[i] = dvalue; else if (keyword == MESO_CV) atom->cv[i] = dvalue; else if (keyword == MESO_RHO) atom->rho[i] = dvalue; + + else if (keyword == EDPD_TEMP) atom->edpd_temp[i] = dvalue; + else if (keyword == EDPD_CV) atom->edpd_cv[i] = dvalue; + else if (keyword == CC) atom->cc[i][cc_index-1] = dvalue; + else if (keyword == SMD_MASS_DENSITY) { // set mass from volume and supplied mass density atom->rmass[i] = atom->vfrac[i] * dvalue; diff --git a/src/set.h b/src/set.h index dfb06a2e12..5584e228ba 100644 --- a/src/set.h +++ b/src/set.h @@ -35,7 +35,8 @@ class Set : protected Pointers { int style,ivalue,newtype,count,index_custom; int ximage,yimage,zimage,ximageflag,yimageflag,zimageflag; double dvalue,xvalue,yvalue,zvalue,wvalue,fraction; - + int cc_index; + int varflag,varflag1,varflag2,varflag3,varflag4; int ivar1,ivar2,ivar3,ivar4; double *vec1,*vec2,*vec3,*vec4;