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
|
||||
|
||||
Reference in New Issue
Block a user