new USER-MESO package
This commit is contained in:
Steve Plimpton
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doc/src/Eqs/fix_mvv_dpd.jpg
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doc/src/Eqs/fix_mvv_dpd.tex
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doc/src/Eqs/fix_mvv_dpd.tex
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\documentclass[12pt]{article}
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\begin{document}
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$$
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v(t+\frac{\Delta t}{2}) = v(t) + \frac{\Delta t}{2}\cdot a(t),
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$$
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$$
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r(t+\Delta t) = r(t) + \Delta t\cdot v(t+\frac{\Delta t}{2}),
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$$
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$$
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a(t+\Delta t) = \frac{1}{m}\cdot F\left[ r(t+\Delta t), v(t) +\lambda \cdot \Delta t\cdot a(t)\right],
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$$
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$$
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v(t+\Delta t) = v(t+\frac{\Delta t}{2}) + \frac{\Delta t}{2}\cdot a(t++\Delta t),
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$$
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\end{document}
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doc/src/Eqs/pair_edpd_force.jpg
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doc/src/Eqs/pair_edpd_force.tex
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doc/src/Eqs/pair_edpd_force.tex
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\documentclass[12pt]{article}
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\begin{document}
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$$
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\mathbf{F}_{ij}^{C} = \alpha_{ij}{\omega_{C}}(r_{ij})\mathbf{e}_{ij},
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$$
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$$
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\mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij},
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$$
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$$
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\mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij},
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$$
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$$
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\omega_{C}(r) = 1 - r/r_c,
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$$
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$$
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\alpha_{ij} = A\cdot k_B(T_i + T_j)/2,
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$$
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$$
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\omega_{D}(r) = \omega^2_{R}(r) = (1-r/r_c)^s,
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$$
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$$
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\sigma_{ij}^2 = 4\gamma k_B T_i T_j/(T_i + T_j),
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$$
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\end{document}
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doc/src/Eqs/pair_edpd_gov.jpg
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doc/src/Eqs/pair_edpd_gov.tex
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doc/src/Eqs/pair_edpd_gov.tex
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\documentclass[12pt]{article}
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\begin{document}
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$$
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\frac{\mathrm{d}^2 \mathbf{r}_i}{\mathrm{d} t^2}=
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\frac{\mathrm{d} \mathbf{v}_i}{\mathrm{d} t}
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=\mathbf{F}_{i}=\sum_{i\neq j}(\mathbf{F}_{ij}^{C}+\mathbf{F}_{ij}^{D}+\mathbf{F}_{ij}^{R}),
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$$
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$$
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C_v\frac{\mathrm{d} T_i}{\mathrm{d} t}= q_{i} = \sum_{i\neq j}(q_{ij}^{C}+q_{ij}^{V}+q_{ij}^{R}),
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$$
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\end{document}
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doc/src/Eqs/pair_edpd_heat.jpg
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doc/src/Eqs/pair_edpd_heat.tex
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doc/src/Eqs/pair_edpd_heat.tex
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\documentclass[12pt]{article}
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\begin{document}
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$$
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q_i^C = \sum_{j \ne i} k_{ij} \omega_{CT}(r_{ij}) \left( \frac{1}{T_i} - \frac{1}{T_j} \right),
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$$
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$$
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q_i^V = \frac{1}{2 C_v}\sum_{j \ne i}{ \left\{ \omega_D(r_{ij})\left[\gamma_{ij} \left( \mathbf{e}_{ij} \cdot \mathbf{v}_{ij} \right)^2 - \frac{\left( \sigma _{ij} \right)^2}{m}\right] - \sigma _{ij} \omega_R(r_{ij})\left( \mathbf{e}_{ij} \cdot \mathbf{v}_{ij} \right){\xi_{ij}} \right\} },
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$$
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$$
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q_i^R = \sum_{j \ne i} \beta _{ij} \omega_{RT}(r_{ij}) d {t^{ - 1/2}} \xi_{ij}^e,
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$$
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$$
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\omega_{CT}(r)=\omega_{RT}^2(r)=\left(1-r/r_{ct}\right)^{s_T},
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$$
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$$
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k_{ij}=C_v^2\kappa(T_i + T_j)^2/4k_B,
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$$
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$$
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\beta_{ij}^2=2k_Bk_{ij},
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$$
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\end{document}
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doc/src/Eqs/pair_edpd_kappa.tex
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doc/src/Eqs/pair_edpd_kappa.tex
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\documentclass[12pt]{article}
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\begin{document}
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$$
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\kappa = \frac{315k_B\upsilon }{2\pi \rho C_v r_{ct}^5}\frac{1}{Pr},
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$$
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\end{document}
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doc/src/Eqs/pair_mdpd_force.tex
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doc/src/Eqs/pair_mdpd_force.tex
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\documentclass[12pt]{article}
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\begin{document}
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$$
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\mathbf{F}_{ij}^C = Aw_c(r_{ij})\mathbf{e}_{ij} + B(\rho_i+\rho_j)w_d(r_{ij})\mathbf{e}_{ij},
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$$
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$$
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\mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij},
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$$
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$$
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\mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij},
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$$
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\end{document}
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doc/src/Eqs/pair_tdpd_flux.jpg
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doc/src/Eqs/pair_tdpd_flux.tex
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doc/src/Eqs/pair_tdpd_flux.tex
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\documentclass[12pt]{article}
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\begin{document}
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$$
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Q_{ij}^D = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right),
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$$
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$$
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Q_{ij}^R = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij},
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$$
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$$
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w_{DC}(r_{ij})=w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power\_{cc}},
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$$
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$$
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\epsilon_{ij}^2 = m_s^2\kappa_{ij}\rho,
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$$
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\end{document}
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doc/src/Eqs/pair_tdpd_force.tex
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doc/src/Eqs/pair_tdpd_force.tex
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\documentclass[12pt]{article}
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\begin{document}
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$$
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\mathbf{F}_{ij}^{C} = A{\omega_{C}}(r_{ij})\mathbf{e}_{ij},
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$$
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$$
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\mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij},
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$$
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$$
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\mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij},
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$$
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$$
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\omega_{C}(r) = 1 - r/r_c,
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$$
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$$
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\omega_{D}(r) = \omega^2_{R}(r) = (1-r/r_c)^{\rm power\_f},
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$$
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$$
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\sigma^2 = 2\gamma k_B T,
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$$
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\end{document}
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doc/src/Eqs/pair_tdpd_gov.jpg
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doc/src/Eqs/pair_tdpd_gov.tex
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doc/src/Eqs/pair_tdpd_gov.tex
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\documentclass[12pt]{article}
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\begin{document}
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$$
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\frac{\mathrm{d}^2 \mathbf{r}_i}{\mathrm{d} t^2} = \frac{\mathrm{d} \mathbf{v}_i}{\mathrm{d} t}=\mathbf{F}_{i}=\sum_{i\neq j}(\mathbf{F}_{ij}^{C}+\mathbf{F}_{ij}^{D}+\mathbf{F}_{ij}^{R}),
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$$
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$$
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\frac{\mathrm{d} C_{i}}{\mathrm{d} t}= Q_{i} = \sum_{i\neq j}(Q_{ij}^{D}+Q_{ij}^{R}) + Q_{i}^{S},
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$$
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\end{document}
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doc/src/JPG/examples_mdpd.gif
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doc/src/JPG/examples_mdpd_first.jpg
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doc/src/JPG/examples_tdpd.jpg
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@ -685,6 +685,7 @@ package"_Section_start.html#start_3.
|
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"drude"_fix_drude.html,
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"drude/transform/direct"_fix_drude_transform.html,
|
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"drude/transform/reverse"_fix_drude_transform.html,
|
||||
"edpd/source"_fix_dpd_source.html,
|
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"eos/cv"_fix_eos_cv.html,
|
||||
"eos/table"_fix_eos_table.html,
|
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"eos/table/rx"_fix_eos_table_rx.html,
|
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@ -704,6 +705,9 @@ package"_Section_start.html#start_3.
|
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"meso"_fix_meso.html,
|
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"manifoldforce"_fix_manifoldforce.html,
|
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"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,
|
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"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,
|
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"dpd"_compute_dpd.html,
|
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"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.
|
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"eam/cd (o)"_pair_eam.html,
|
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"edip (o)"_pair_edip.html,
|
||||
"edip/multi"_pair_edip.html,
|
||||
"edpd"_pair_meso.html,
|
||||
"eff/cut"_pair_eff.html,
|
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"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)
|
||||
|
||||
@ -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:]
|
||||
|
||||
@ -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.
|
||||
|
||||
61
doc/src/compute_edpd_temp_atom.txt
Normal file
61
doc/src/compute_edpd_temp_atom.txt
Normal file
@ -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.
|
||||
|
||||
60
doc/src/compute_tdpd_cc_atom.txt
Normal file
60
doc/src/compute_tdpd_cc_atom.txt
Normal file
@ -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
|
||||
|
||||
101
doc/src/fix_dpd_source.txt
Normal file
101
doc/src/fix_dpd_source.txt
Normal file
@ -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
|
||||
97
doc/src/fix_mvv_dpd.txt
Normal file
97
doc/src/fix_mvv_dpd.txt
Normal file
@ -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 <font size="4">λ</font> 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
|
||||
|
||||
277
doc/src/pair_meso.txt
Normal file
277
doc/src/pair_meso.txt
Normal file
@ -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 <font size="4">F<sub>i</sub></font>
|
||||
including the conservative force <font
|
||||
size="4">F<sub>ij</sub><sup>C</sup></font>, dissipative force <font
|
||||
size="4">F<sub>ij</sub><sup>D</sup></font> and random force <font
|
||||
size="4">F<sub>ij</sub><sup>R</sup></font> are expressed as
|
||||
|
||||
:c,image(Eqs/pair_edpd_force.jpg)
|
||||
|
||||
in which the exponent of the weighting function <font
|
||||
size="4"><i>s</i></font> can be defined as a temperature-dependent
|
||||
variable. The heat flux between particles accounting for the
|
||||
collisional heat flux <font size="4">q<sup>C</sup></font>, viscous
|
||||
heat flux <font size="4">q<sup>V</sup></font>, and random heat flux
|
||||
<font size="4">q<sup>R</sup></font> are given by
|
||||
|
||||
:c,image(Eqs/pair_edpd_heat.jpg)
|
||||
|
||||
where the mesoscopic heat friction <font size="4">κ</font> is given by
|
||||
|
||||
:c,image(Eqs/pair_edpd_kappa.jpg)
|
||||
|
||||
with <font size="4">υ</font> 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 <font size="4">c<sub>1</sub>, c<sub>2</sub>,
|
||||
c<sub>4</sub>, c<sub>4</sub></font> showing the temperature dependence
|
||||
of the exponent <center><font size="4"> <i>s</i>(<i>T</i>) =
|
||||
power_f*(1+c<sub>1</sub>*(T-1)+c<sub>2</sub>*(T-1)<sup>2</sup>
|
||||
+c<sub>3</sub>*(T-1)<sup>3</sup>+c<sub>4</sub>*(T-1)<sup>4</sup>)</font></center>
|
||||
and of the mesoscopic heat friction <center><font size="4">
|
||||
<i>s<sub>T</sub>(T)</i> =
|
||||
kappa*(1+c<sub>1</sub>*(T-1)+c<sub>2</sub>*(T-1)<sup>2</sup>
|
||||
+c<sub>3</sub>*(T-1)<sup>3</sup>+c<sub>4</sub>*(T-1)<sup>4</sup>)</font></center>
|
||||
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 <font size="4">F<sup>C</sup></font> with a
|
||||
negative coefficient A < 0 stands for an attractive force within an
|
||||
interaction range <font size="4">r<sub>c</sub></font>, and the second
|
||||
term with B > 0 is the density-dependent repulsive force within an
|
||||
interaction range <font size="4">r<sub>d</sub></font>.
|
||||
|
||||
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 <font size="4">F<sub>i</sub></font>
|
||||
including the conservative force <font
|
||||
size="4">F<sub>ij</sub><sup>C</sup></font>, dissipative force <font
|
||||
size="4">F<sub>ij</sub><sup>D</sup></font> and random force <font
|
||||
size="4">F<sub>ij</sub><sup>R</sup></font> are expressed as
|
||||
|
||||
:c,image(Eqs/pair_tdpd_force.jpg)
|
||||
|
||||
The concentration flux between two tDPD particles includes the Fickian
|
||||
flux <font size="4">Q<sub>ij</sub><sup>D</sup></font> and random flux
|
||||
<font size="4">Q<sub>ij</sub><sup>R</sup></font>, 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. <font size="4"><i>m</i><sub>s</sub></font>
|
||||
is the mass of a single solute molecule. In general, <font
|
||||
size="4"><i>m</i><sub>s</sub></font> is much smaller than the mass of
|
||||
a tDPD particle <font size="4"><i>m</i></font>. 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.
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
40
examples/USER/meso/README
Normal file
40
examples/USER/meso/README
Normal file
@ -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
|
||||
54
examples/USER/meso/edpd/in.edpd
Normal file
54
examples/USER/meso/edpd/in.edpd
Normal file
@ -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
|
||||
142
examples/USER/meso/edpd/log.16Aug17.edpd.g++.1
Normal file
142
examples/USER/meso/edpd/log.16Aug17.edpd.g++.1
Normal file
@ -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
|
||||
142
examples/USER/meso/edpd/log.16Aug17.edpd.g++.4
Normal file
142
examples/USER/meso/edpd/log.16Aug17.edpd.g++.4
Normal file
@ -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
|
||||
24
examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.1
Normal file
24
examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.1
Normal file
@ -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
|
||||
24
examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.4
Normal file
24
examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.4
Normal file
@ -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
|
||||
52
examples/USER/meso/mdpd/in.mdpd
Normal file
52
examples/USER/meso/mdpd/in.mdpd
Normal file
@ -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
|
||||
147
examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.1
Normal file
147
examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.1
Normal file
@ -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
|
||||
147
examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.4
Normal file
147
examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.4
Normal file
@ -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
|
||||
24
examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.1
Normal file
24
examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.1
Normal file
@ -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
|
||||
24
examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.4
Normal file
24
examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.4
Normal file
@ -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
|
||||
54
examples/USER/meso/tdpd/in.tdpd
Normal file
54
examples/USER/meso/tdpd/in.tdpd
Normal file
@ -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
|
||||
146
examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.1
Normal file
146
examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.1
Normal file
@ -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
|
||||
146
examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.4
Normal file
146
examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.4
Normal file
@ -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
|
||||
@ -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
|
||||
|
||||
50
src/USER-MESO/README
Normal file
50
src/USER-MESO/README
Normal file
@ -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.
|
||||
844
src/USER-MESO/atom_vec_edpd.cpp
Normal file
844
src/USER-MESO/atom_vec_edpd.cpp
Normal file
@ -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 <string.h>
|
||||
#include <stdlib.h>
|
||||
#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<int> (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;
|
||||
}
|
||||
68
src/USER-MESO/atom_vec_edpd.h
Normal file
68
src/USER-MESO/atom_vec_edpd.h
Normal file
@ -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
|
||||
951
src/USER-MESO/atom_vec_mdpd.cpp
Normal file
951
src/USER-MESO/atom_vec_mdpd.cpp
Normal file
@ -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 <string.h>
|
||||
#include <stdlib.h>
|
||||
#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<int> (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;
|
||||
}
|
||||
79
src/USER-MESO/atom_vec_mdpd.h
Normal file
79
src/USER-MESO/atom_vec_mdpd.h
Normal file
@ -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
|
||||
879
src/USER-MESO/atom_vec_tdpd.cpp
Normal file
879
src/USER-MESO/atom_vec_tdpd.cpp
Normal file
@ -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 <string.h>
|
||||
#include <stdlib.h>
|
||||
#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<int> (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;
|
||||
}
|
||||
83
src/USER-MESO/atom_vec_tdpd.h
Normal file
83
src/USER-MESO/atom_vec_tdpd.h
Normal file
@ -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.
|
||||
|
||||
*/
|
||||
97
src/USER-MESO/compute_edpd_temp_atom.cpp
Normal file
97
src/USER-MESO/compute_edpd_temp_atom.cpp
Normal file
@ -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 <string.h>
|
||||
#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;
|
||||
}
|
||||
43
src/USER-MESO/compute_edpd_temp_atom.h
Normal file
43
src/USER-MESO/compute_edpd_temp_atom.h
Normal file
@ -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
|
||||
98
src/USER-MESO/compute_tdpd_cc_atom.cpp
Normal file
98
src/USER-MESO/compute_tdpd_cc_atom.cpp
Normal file
@ -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 <string.h>
|
||||
#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;
|
||||
}
|
||||
44
src/USER-MESO/compute_tdpd_cc_atom.h
Normal file
44
src/USER-MESO/compute_tdpd_cc_atom.h
Normal file
@ -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
|
||||
120
src/USER-MESO/fix_edpd_source.cpp
Normal file
120
src/USER-MESO/fix_edpd_source.cpp
Normal file
@ -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 <stdlib.h>
|
||||
#include <string.h>
|
||||
#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];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
44
src/USER-MESO/fix_edpd_source.h
Normal file
44
src/USER-MESO/fix_edpd_source.h
Normal file
@ -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
|
||||
136
src/USER-MESO/fix_mvv_dpd.cpp
Normal file
136
src/USER-MESO/fix_mvv_dpd.cpp
Normal file
@ -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 <stdio.h>
|
||||
#include <string.h>
|
||||
#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;
|
||||
}
|
||||
45
src/USER-MESO/fix_mvv_dpd.h
Normal file
45
src/USER-MESO/fix_mvv_dpd.h
Normal file
@ -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
|
||||
163
src/USER-MESO/fix_mvv_edpd.cpp
Normal file
163
src/USER-MESO/fix_mvv_edpd.cpp
Normal file
@ -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 <stdio.h>
|
||||
#include <string.h>
|
||||
#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;
|
||||
}
|
||||
45
src/USER-MESO/fix_mvv_edpd.h
Normal file
45
src/USER-MESO/fix_mvv_edpd.h
Normal file
@ -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
|
||||
156
src/USER-MESO/fix_mvv_tdpd.cpp
Normal file
156
src/USER-MESO/fix_mvv_tdpd.cpp
Normal file
@ -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 <stdio.h>
|
||||
#include <string.h>
|
||||
#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;
|
||||
}
|
||||
46
src/USER-MESO/fix_mvv_tdpd.h
Normal file
46
src/USER-MESO/fix_mvv_tdpd.h
Normal file
@ -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
|
||||
120
src/USER-MESO/fix_tdpd_source.cpp
Normal file
120
src/USER-MESO/fix_tdpd_source.cpp
Normal file
@ -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 <stdlib.h>
|
||||
#include <string.h>
|
||||
#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;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
45
src/USER-MESO/fix_tdpd_source.h
Normal file
45
src/USER-MESO/fix_tdpd_source.h
Normal file
@ -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
|
||||
551
src/USER-MESO/pair_edpd.cpp
Normal file
551
src/USER-MESO/pair_edpd.cpp
Normal file
@ -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 <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#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 <time.h>
|
||||
#include <string.h>
|
||||
|
||||
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;
|
||||
}
|
||||
85
src/USER-MESO/pair_edpd.h
Normal file
85
src/USER-MESO/pair_edpd.h
Normal file
@ -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.
|
||||
|
||||
*/
|
||||
425
src/USER-MESO/pair_mdpd.cpp
Normal file
425
src/USER-MESO/pair_mdpd.cpp
Normal file
@ -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 <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#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 <time.h>
|
||||
|
||||
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]);
|
||||
}
|
||||
|
||||
84
src/USER-MESO/pair_mdpd.h
Normal file
84
src/USER-MESO/pair_mdpd.h
Normal file
@ -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.
|
||||
|
||||
*/
|
||||
267
src/USER-MESO/pair_mdpd_rhosum.cpp
Normal file
267
src/USER-MESO/pair_mdpd_rhosum.cpp
Normal file
@ -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 <math.h>
|
||||
#include <stdlib.h>
|
||||
#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++];
|
||||
}
|
||||
50
src/USER-MESO/pair_mdpd_rhosum.h
Normal file
50
src/USER-MESO/pair_mdpd_rhosum.h
Normal file
@ -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
|
||||
477
src/USER-MESO/pair_tdpd.cpp
Normal file
477
src/USER-MESO/pair_tdpd.cpp
Normal file
@ -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 <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#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 <time.h>
|
||||
|
||||
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; k<cc_species; k++) {
|
||||
double wcr = 1.0 - r/cutcc[itype][jtype];
|
||||
wcr = MAX(0,wcr);
|
||||
wcr = pow(wcr, 0.5*powercc[itype][jtype][k]);
|
||||
double randnum = random->gaussian();
|
||||
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; k<cc_species; k++) {
|
||||
kappa_one[k] = force->numeric(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; k<cc_species; k++)
|
||||
{
|
||||
kappa [i][j][k] = kappa_one[k];
|
||||
epsilon[i][j][k]= epsilon_one[k];
|
||||
powercc[i][j][k]= powercc_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 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; k<cc_species; k++) {
|
||||
kappa[j][i][k] = kappa[i][j][k];
|
||||
epsilon[j][i][k] = epsilon[i][j][k];
|
||||
powercc[j][i][k] = powercc[i][j][k];
|
||||
}
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairTDPD::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(&cutcc[i][j],sizeof(double),1,fp);
|
||||
for(int k=0; k<cc_species; k++) {
|
||||
fwrite(&kappa[i][j][k],sizeof(double),1,fp);
|
||||
fwrite(&epsilon[i][j][k],sizeof(double),1,fp);
|
||||
fwrite(&powercc[i][j][k],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairTDPD::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(&cutcc[i][j],sizeof(double),1,fp);
|
||||
for(int k=0; k<cc_species; k++) {
|
||||
fread(&kappa[i][j][k],sizeof(double),1,fp);
|
||||
fread(&epsilon[i][j][k],sizeof(double),1,fp);
|
||||
fread(&powercc[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(&cutcc[i][j],1,MPI_DOUBLE,0,world);
|
||||
for(int k=0; k<cc_species; k++) {
|
||||
MPI_Bcast(&kappa[i][j][k],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&epsilon[i][j][k],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&powercc[i][j][k],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairTDPD::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 PairTDPD::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);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
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;
|
||||
}
|
||||
81
src/USER-MESO/pair_tdpd.h
Normal file
81
src/USER-MESO/pair_tdpd.h
Normal file
@ -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.
|
||||
|
||||
*/
|
||||
14
src/atom.cpp
14
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;
|
||||
}
|
||||
|
||||
@ -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
|
||||
|
||||
|
||||
72
src/set.cpp
72
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;
|
||||
|
||||
@ -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;
|
||||
|
||||
Reference in New Issue
Block a user