Loading doc/src/compute_edpd_temp_atom.txt +3 −2 Original line number Diff line number Diff line Loading @@ -26,7 +26,8 @@ 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. For more details please see "(Espanol1997)"_#Espanol1997 and "(Li2014)"_#Li2014a. [Output info:] Loading Loading @@ -55,7 +56,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. [(Espanol1997)] Espanol, Europhys Lett, 40(6): 631-636 (1997). DOI: 10.1209/epl/i1997-00515-8 :link(Li2014) :link(Li2014a) [(Li2014)] Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003. doc/src/compute_tdpd_cc_atom.txt +2 −2 Original line number Diff line number Diff line Loading @@ -28,7 +28,7 @@ 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. details see "(Li2015)"_#Li2015a. [Output info:] Loading @@ -54,7 +54,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. :line :link(Li2015) :link(Li2015a) [(Li2015)] Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI: 10.1063/1.4923254 doc/src/computes.txt +2 −0 Original line number Diff line number Diff line Loading @@ -30,6 +30,7 @@ Computes :h1 compute_displace_atom compute_dpd compute_dpd_atom compute_edpd_temp_atom compute_erotate_asphere compute_erotate_rigid compute_erotate_sphere Loading Loading @@ -95,6 +96,7 @@ Computes :h1 compute_sna_atom compute_stress_atom compute_tally compute_tdpd_cc_atom compute_temp compute_temp_asphere compute_temp_body Loading doc/src/fix_dpd_source.txt +4 −4 Original line number Diff line number Diff line Loading @@ -46,8 +46,8 @@ 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 heat conduction with a source term (see Fig.12 in "(Li2014)"_#Li2014b) or diffusion with a source term (see Fig.1 in "(Li2015)"_#Li2015b), as an analog of a periodic Poiseuille flow problem. If the {sphere} keyword is used, the {cx,cy,cz,radius} defines a Loading Loading @@ -88,13 +88,13 @@ tdpd/cc/atom"_compute_tdpd_cc_atom.html :line :link(Li2014) :link(Li2014b) [(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) :link(Li2015b) [(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 Loading doc/src/fix_mvv_dpd.txt +2 −2 Original line number Diff line number Diff line Loading @@ -48,7 +48,7 @@ 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. "Groot"_#Groot2. 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 Loading Loading @@ -91,7 +91,7 @@ The default value for the optional {lambda} parameter is 0.5. :line :link(Groot) :link(Groot2) [(Groot)] Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI: 10.1063/1.474784 Loading
doc/src/compute_edpd_temp_atom.txt +3 −2 Original line number Diff line number Diff line Loading @@ -26,7 +26,8 @@ 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. For more details please see "(Espanol1997)"_#Espanol1997 and "(Li2014)"_#Li2014a. [Output info:] Loading Loading @@ -55,7 +56,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. [(Espanol1997)] Espanol, Europhys Lett, 40(6): 631-636 (1997). DOI: 10.1209/epl/i1997-00515-8 :link(Li2014) :link(Li2014a) [(Li2014)] Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003.
doc/src/compute_tdpd_cc_atom.txt +2 −2 Original line number Diff line number Diff line Loading @@ -28,7 +28,7 @@ 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. details see "(Li2015)"_#Li2015a. [Output info:] Loading @@ -54,7 +54,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. :line :link(Li2015) :link(Li2015a) [(Li2015)] Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI: 10.1063/1.4923254
doc/src/computes.txt +2 −0 Original line number Diff line number Diff line Loading @@ -30,6 +30,7 @@ Computes :h1 compute_displace_atom compute_dpd compute_dpd_atom compute_edpd_temp_atom compute_erotate_asphere compute_erotate_rigid compute_erotate_sphere Loading Loading @@ -95,6 +96,7 @@ Computes :h1 compute_sna_atom compute_stress_atom compute_tally compute_tdpd_cc_atom compute_temp compute_temp_asphere compute_temp_body Loading
doc/src/fix_dpd_source.txt +4 −4 Original line number Diff line number Diff line Loading @@ -46,8 +46,8 @@ 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 heat conduction with a source term (see Fig.12 in "(Li2014)"_#Li2014b) or diffusion with a source term (see Fig.1 in "(Li2015)"_#Li2015b), as an analog of a periodic Poiseuille flow problem. If the {sphere} keyword is used, the {cx,cy,cz,radius} defines a Loading Loading @@ -88,13 +88,13 @@ tdpd/cc/atom"_compute_tdpd_cc_atom.html :line :link(Li2014) :link(Li2014b) [(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) :link(Li2015b) [(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 Loading
doc/src/fix_mvv_dpd.txt +2 −2 Original line number Diff line number Diff line Loading @@ -48,7 +48,7 @@ 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. "Groot"_#Groot2. 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 Loading Loading @@ -91,7 +91,7 @@ The default value for the optional {lambda} parameter is 0.5. :line :link(Groot) :link(Groot2) [(Groot)] Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI: 10.1063/1.474784
