File List
Here is a list of all documented files with brief descriptions:
| BC10_FMT1_WCA_ELEC_3D/README [code] | 3D case - testing periodic boundaries in y and z coupled with a reflective boundary in the RHS of x |
| BC11_FMT1_WCA_ELEC_3D/README [code] | 3D case - testing continuation boundaries in y and z coupled with a reflective boundary in the RHS of x |
| BC12_FMT1_WCA_ELEC_3D/README [code] | 3D case - testing continuation boundaries in y and reflective boundaries in z as wellas the RHS of x |
| BC1_FMT1_WCA_ELEC_2D/README [code] | 2D case - testing reflective boundaries in y direction with complex physics |
| BC2_FMT1_WCA_ELEC_2D/README [code] | 2D case - testing reflective boundaries in x direction with complex physics |
| BC3_FMT1_WCA_ELEC_2D/README [code] | 2D case - testing periodic boundaries in y direction with complex physics |
| BC4_FMT1_WCA_ELEC_2D/README [code] | 2D case - testing periodic boundaries in x direction with complex physics |
| BC5_FMT1_WCA_ELEC_2D/README [code] | 2D case - testing continuation boundaries in y direction with complex physics |
| BC6_FMT1_WCA_ELEC_2D/README [code] | 2D case - testing continuation boundaries in x direction with complex physics |
| BC7_FMT1_WCA_ELEC_3D/README [code] | 3D case - testing reflective boundaries in y and z and RHS of x |
| BC8_FMT1_WCA_ELEC_3D/README [code] | 3D case - testing reflective boundaries in x and z and RHS of y |
| BC9_FMT1_WCA_ELEC_3D/README [code] | 3D case - testing reflective boundaries in x and y and LHS of z |
| BULK1_FMT1_WCA_1D/README [code] | 1D case - locate a binodal approximately with Arc-Length continuation. One component Liquid-Vapor equilibrium |
| BULK2_FMT1_WCA_1D/README [code] | 1D case - locate binodal precisely with binodal tracking algorithm (LOCA). One component Liquid-Vapor equilibrium |
| BULK3_FMT1_WCA_1D/README [code] | 1D case - compute structure of liquid-vapor interface |
| BULK4_MIX_FMT3_WCA_WJDC_1D/README [code] | 1D case - locate a binodal approximately with Arc-Length continuation. Two component Liquid-Vapor equilibrium |
| BULK5_MIX_FMT3_WCA_WJDC_1D/README [code] | 1D case - locate binodal precisely with binodal tracking algorithm (LOCA), and create Pxy data for two component liquid-vapor equilibrium |
| BULK6_MIX_FMT3_WCA_WJDC_1D/README [code] | 1D case - compute structure of liquid-vapor interface for a TWO component system |
| BULK7_FMT3_WCA_WJDC_1D/README [code] | Liquid-Vapor Equilibria in 8-mer chain system (1D) |
| BULK8_MIX_FMT3_WCA_WJDC_1D/README [code] | Paritioning calcualtion for a system composed of an 8-mer chain and a single site solvent (1D) |
| CONT1_FMT1_WCA_1D/README [code] | 1D case - testing continuation algorithms (LOCA library) |
| CONT2_FMT1_WCA_1D/README [code] | 1D case - testing continuation algorithms (LOCA library) |
| CONT3_FMT1_WCA_1D/README [code] | 1D case - testing spinodal continuation (LOCA library) |
| CONT4_FMT1_WCA_1D/README [code] | 1D case - testing binodal continuation (LOCA library) |
| DIFFUSION1_FMT1_WCA_1D/README [code] | Color diffusion of an atomistic fluid through a permeable membrane |
| DIFFUSION2_FMT1_WCA_WJDC_1D/README [code] | Color diffusion (Fickian) of a bonded chain fluid through a permeable membrane |
| DIFFUSION3_FMT1_WCA_PICARD_1D/README [code] | Color diffusion of an atomistic fluid through a permeable membrane. Test for picard solver with diffusion problem |
| DIFFUSION4_FMT1_WCA_3D/README [code] | Color diffusion of an atomistic fluid through a permeable membrane - 3D calculation |
| DIFFUSION5_FMT1_WCA_WJDC_3D/README [code] | Color diffusion (Fickian) of a bonded chain fluid through a permeable membrane for a 3D system |
| DIFFUSION6_FMT1_WCA_PICARD_3D/README [code] | Color diffusion of an atomistic fluid through a permeable membrane - 3D calculation with Picard solver |
| EXP_FMT3_1D/README [code] | Cut and shifted exponential attraction |
| GEOM10_SPHERE_3D/README [code] | 3D spherical surfaces. Vext(integrated) |
| GEOM11_CYL_2D/README [code] | 2D infinite cylindrical surfaces. Vext(integrated) |
| GEOM12_CYL_2D/README [code] | 2D infinite cylindrical surfaces. Vext(integrated) |
| GEOM13_CYL_ROUGH_2D/README [code] | 2D rough infinite cylindrical surfaces. Vext(integrated) |
| GEOM14_CYL_WEDGECUTOUT_2D/README [code] | 2D infinite cylindrical surfaces with a wedge removed. Vext(integrated) |
| GEOM15_CYL_WEDGE2TYPES_2D/README [code] | 2D infinite cylindrical surfaces with wedges removed. compound surfaces are created by putting pairs of complementary wedges together. Vext(integrated) |
| GEOM16_CYL_WEDGE2TYPES_REFLECT_2D/README [code] | 2D infinite cylindrical surfaces with wedges removed. compound surfaces are created by putting pairs of complementary wedges together. Vext(integrated). Reflective boundaries |
| GEOM17_1ELEM_1D/README [code] | 1D 1element (thin membrane) surfaces |
| GEOM18_1ELEM_2D/README [code] | 2D 1element (thin rod) surfaces |
| GEOM19_1ELEM_3D/README [code] | 3D 1element (point) surfaces |
| GEOM1_PLANE_ROUGH_2D/README [code] | 2D rough planar walls perpendicular to x axis. / Vext(Xwall) |
| GEOM20_CYL_3D/README [code] | 3D finite length cylindrical surfaces. Vext(integrated) |
| GEOM21_CYL_ROUGH_3D/README [code] | 3D finite length rough cylindrical surfaces. Vext(integrated) |
| GEOM22_CYL_WEDGE2TYPES_3D/README [code] | 3D infinite length compound cylindrical wedge surfaces. Two total surfaces each composed of two surface types. Vext(integrated) |
| GEOM23_CYL_PERIODIC_3D/README [code] | 3D infinite length periodic cylindrical surfaces. Vext(integrated) |
| GEOM24_ATOMS_3D/README [code] | 3D atomistic surface based on 10-mer chain. Vext(integrated) |
| GEOM25_CYL_PORE_2D/README [code] | 2D cylindrical pore. Vext(integrated) |
| GEOM26_CYL_PORE_ROUGH_2D/README [code] | 2D rough cylindrical pore. Vext(integrated) |
| GEOM27_CYL_PORE_WEDGE2TYPES_2D/README [code] | 2D rough compound cylindrical pore surface with two types of surface-fluid chemistry. Vext(integrated) |
| GEOM28_CYLPORE_WEDGE2TYPES_3D/README [code] | 3D rough compound cylindrical finite-length pore with two types of surface-fluid chemistry. Vext(integrated) |
| GEOM29_SLITPORE_2D/README [code] | 2D slit pore of finite length. One wall is smooth, the other is rough. Ncomp=2; Vext(integrated) |
| GEOM2_PLANE_ROUGH_2D/README [code] | 2D rough planar walls perpendicular to y axis. / Vext(Xwall) |
| GEOM30_TAPERED_SLITPORE_2D/README [code] | 2D tapered slit pore of finite length. Ncomp=2; Vext(integrated) |
| GEOM31_TAPERED_CYLPORE_3D/README [code] | 3D tapered cylindrical pore of finite length. Ncomp=1; Vext(integrated) |
| GEOM32_PLANE_PERIODIC_2D/README [code] | 2D surface with superimposed periodic function (corrugated surface) |
| GEOM33_PLANE_PERIODIC2_2D/README [code] | 2D surface with superimposed periodic function (corrugated surface). Orientation test |
| GEOM34_PLANE_PERIODIC3_2D/README [code] | 2D surface with two superimposed periodic functions (corrugated surface) |
| GEOM35_PLANE_PERIODIC_3D/README [code] | 3D surface with two superimposed periodic functions in different directions (egg-carton surface) |
| GEOM36_PLANE_NOTCH_2D/README [code] | 2D surface with a notch removed from the surface. Charged surface with electrolyte |
| GEOM37_WEDGE_LINEAR_2D/README [code] | 2D wedge surface constructed with linear functions superimposed on a plane. Vext(integrated) |
| GEOM38_WEDGE_3D/README [code] | 3D wedge surface in 3D constructed with 4 linear functions superimposed on a plane. Vext(integrated) |
| GEOM39_AMFTIP_3D/README [code] | 3D model of a small AFM tip with a square pyramid structure |
| GEOM3_PLANE_ROUGH_3D/README [code] | 3D / rough planar surfaces / perpendicular to x axis. / Vext(Xwall) |
| GEOM40_AMFTIP_HEMISPHERE_3D/README [code] | 3D model of a small AFM tip with a hemispherical tip structure |
| GEOM4_PLANE_ROUGH_3D/README [code] | 3D case / rough planar surfaces / perpendicular to y axis. / Vext(Xwall) |
| GEOM5_PLANE_ROUGH_3D/README [code] | 3D / rough planar surfaces / perpendicular to z axis. / Vext(Xwall) |
| GEOM6_PLANE_ROUGH_VEXTINT_2D/README [code] | 2D rough planar walls perpendicular to x axis. / Vext(integrated) |
| GEOM7_PLANE_ROUGH_VEXTINT_3D/README [code] | 3D rough planar walls perpendicular to x axis. / Vext(integrated) |
| GEOM8_BLOCK_2D/README [code] | 2D finite block surfaces. Vext(integrated) |
| GEOM9_BLOCK_3D/README [code] | 3D finite block surfaces. Vext(integrated) |
| HS1_FMT1_1D/README [code] | Hard sphere fluid in a hard wall slit (high resolution) |
| HS2_FMT1_1D/README [code] | Hard sphere fluid in a hard wall slit (low resolution) |
| HS3_FMT1_1D/README [code] | Hard sphere fluid in a hard wall slit (left reflecting boundary) |
| HS4_FMT1_1D/README [code] | Hard sphere fluid in a hard wall slit (right reflecting boundary) |
| HS5_FMT1_1D/README [code] | Hard sphere fluid near one hard wall |
| HS6_FMT1_1D/README [code] | Hard sphere fluid near one hard wall (4 mesh coarsening zones) |
| HS7_FMT1_1D/README [code] | Hard sphere fluid near one hard wall (residual and Jacobian coarsening) |
| HS8_FMT4_1D/README [code] | Hard sphere fluid in a hard wall slit (high resolution) |
| LJ1_FMT1_WCA_1D/README [code] | Lennard-Jones fluid at high density |
| LJ2_FMT1_WCA_1D/README [code] | Lennard-Jones fluid at high density - Test mixing rule |
| LJ3_FMT1_WCA_1D/README [code] | Lennard-Jones fluid at high density - Long range wall-fluid potential |
| LJ4_FMT1_WCA_1D/README [code] | Lennard-Jones fluid at high density - Test numerical integration of wall potential |
| LJ5_FMT1_WCA2_1D/README [code] | Lennard-Jones fluid at high density |
| MIX10_FMT1_ATTELEC_1D/README [code] | Primitive model electrolyte (2 components) |
| MIX11_FMT1_WCA_1D/README [code] | Lennard-Jones mixture (2 components) |
| MIX12_FMT1_ELEC_1D/README [code] | Primitive model electrolyte (2 components) with corrections |
| MIX13_ELEC_PICARD_1D/README [code] | Poisson-Boltzmann electrolyte (2 components). Test Picard Solver |
| MIX1_FMT1_1D/README [code] | Hard Sphere mixture (2 components) |
| MIX2_FMT1_WCA_1D/README [code] | Lennard-Jones mixture (2 components) |
| MIX3_ELEC_1D/README [code] | Poisson-Boltzmann electrolyte (2 components) |
| MIX4_FMT1_ELEC_1D/README [code] | Primitive model electrolyte (2 components) |
| MIX5_FMT1_ELEC_1D/README [code] | Primitive model electrolyte (2 components) with corrections |
| MIX6_FMT1_ELEC_1D/README [code] | Civilized model electrolyte (3 components) |
| MIX7_FMT1_WCA_ELEC_1D/README [code] | Lennard-Jones electrolyte (3 components) |
| MIX8_FMT1_WCA_ELEC_1D/README [code] | Lennard-Jones electrolyte (3 components) with a coarse mesh |
| MIX9_FMT1_WCA_ELEC_1D/README [code] | Lennard-Jones electrolyte (3 components) coarse mesh,small domain |
| NLSOLVER1_WJDC_FMT3_1D/README [code] | NL_Solver=0 8-2-8 hard polymer at a hard wall |
| NLSOLVER2_WJDC_FMT3_1D/README [code] | NL_Solver=1 8-2-8 hard polymer at a hard wall |
| NLSOLVER3_WJDC_FMT3_1D/README [code] | NL_Solver=2 8-2-8 hard polymer at a hard wall |
| NLSOLVER4_WJDC_FMT3_1D/README [code] | NL_Solver=3; 8-2-8 hard polymer at a hard wall |
| NLSOLVER5_WJDC_FMT3_1D/README [code] | NL_Solver=4 8-2-8 hard polymer at a hard wall |
| POLY10_WJDC_FMT1_1D/README [code] | WJDC functionals: 5-mer at a hard wall |
| POLY11_WJDC_FMT1_1D/README [code] | WJDC functionals: 5-mer at a hard wall |
| POLY12_WJDC_FMT1_1D/README [code] | WJDC functionals: blocked polymer blend |
| POLY13_WJDC_FMT1_WCA_1D/README [code] | 8-2-8 hard polymer at a hard wall |
| POLY14_WJDC_FMT1_WCA_1D/README [code] | 8-2-8 hard polymer at a hard wall |
| POLY15_WJDC_FMT3_1D/README [code] | WJDC functionals: 5-mer at a hard wall |
| POLY16_WJDC_FMT3_1D/README [code] | WJDC functionals: 5-mer at a hard wall |
| POLY17_WJDC_FMT3_1D/README [code] | WJDC functionals: blocked polymer blend |
| POLY18_WJDC_FMT3_1D/README [code] | 8-2-8 hard polymer at a hard wall |
| POLY19_WJDC_FMT3_1D/README [code] | Symmetric 8-2-8 hard polymer at a hard wall |
| POLY1_CMS_1D/README [code] | 8-2-8 hard polymer at a hard wall |
| POLY20_CMS_1D/README [code] | Lipid bilayer: 8-2-8 lipid plus solvent |
| POLY21_WJDC_FMT3_1D/README [code] | Symmetric 8-2-8 hard polymer at a hard wall |
| POLY22_WJDC_FMT3_1D/README [code] | Symmetric 8-2-8 hard polymer at a hard wall |
| POLY24_CMS_GRAFT_1D/README [code] | Grafted, length 10 CMS polymer grafted to a hard wall |
| POLY25_WJDC_FMT3_ELEC/README [code] | WJDC functionals: charged 10-mer and single site counterions at a hard wall |
| POLY26_WJDC_FMT3_ELEC/README [code] | WJDC functionals: charged 10-mer and single site counterions in a hard wall slit |
| POLY27_WJDC_FMT3_ELEC/README [code] | WJDC functionals: charged 10-mer and single site counterions in a hard wall slit |
| POLY28_WJDC_FMT3_ELEC/README [code] | WJDC functionals: charged 10-mer and single site counterions in a hard wall slit |
| POLY2_CMS_1D/README [code] | 8-2-8 attractive polymer at a 9-3 Lennard-Jones wall |
| POLY3_CMS_1D/README [code] | Lipid bilayer: 8-2-8 lipid plus solvent |
| POLY4_CMS_1D/README [code] | Charged Lipid bilayer: 8-2-8 lipid plus solvent |
| POLY5_WTC_FMT1_1D/README [code] | WTC functionals: 3-mer at a hard wall |
| POLY6_WTC_FMT1_1D/README [code] | WTC functionals: 5-mer at a hard wall |
| POLY7_WTC_FMT1_1D/README [code] | WTC functionals: blocked 5-mer at a hard wall |
| POLY8_WTC_FMT1_ELEC_1D/README [code] | WTC functionals: 5-mer at a hard wall with electrostatics |
| POLY9_WTC_FMT1_1D/README [code] | WTC functionals: blocked polymer blend |
| POLYBRANCH1_WJDC_FMT3_1D/README [code] | Branched WJDC polymer. Case is identical to 3-arm star case from Jain-Chapman 2009 manuscript |
| POLYGRAFT1_WJDC_JAINPAPER_1D/README [code] | Grafted, length 50 hard polymer grafted to a hard wall |
| POLYGRAFT2_WJDC_1D/README [code] | Grafted 50mer polymer attached to a noninteracting wall |
| POLYGRAFT3_WJDC_SEMIGRAND_1D/README [code] | Grafted 10-mer polymer: end graft to a noninteracting wall. This case includes a free solvent |
| POLYGRAFT4_WJDC_MIDSEG_1D/README [code] | Grafted 49mer polymer attached to a noninteracting wall. This chain is grafted at segment 24 (the middle of the chain) rather than at the end |
| POLYGRAFT5_WJDC_ATT_MIXTURE_1D/README [code] | Mixture of grafted chains at different walls with attractions, external field, and midpoint grafting |
| POLYGRAFT6_WJDC_2SURF_2D/README [code] | Mixture of two types of grafted chains on cylindrical walls in a 2D system, One chain is end grafted, the other is not |
| SELF_ASSEMBLE1_FMT3_WCA_WJDC_1D/README [code] | Lipid bilayer system based on 8-2-8 lipid and single site solvent (1D) using Jain, Dominik, Chapman functionals |
| SELF_ASSEMBLE2_FMT3_WCA_WJDC_1D/README [code] | A test of mesh continuation and the force sum rule using a calculatoin of a confined lipid bilayer system based on 8-2-8 lipid and single site solvent (1D). These calculations use the Jain, Dominik, Chapman functionals |
| SELF_ASSEMBLE3_FMT3_WCA_WJDC_1D/README [code] | Phase transition tracking of confined lipid assemblies (bilayer/SAM) using 8-2-8 lipid and single site solvent |
| SELF_ASSEMBLE4_FMT3_WCA_WJDC_1D/README [code] | Oil/water/surfactant interface |
| SELF_ASSEMBLE5_BILAYERS_4MERTAIL/README [code] | Oil/water/surfactant interface |
| SELF_ASSEMBLE6_BILAYERS_8MERTAIL/README [code] | Oil/water/surfactant interface |
| SELF_ASSEMBLE7_BILAYERS_16MERTAIL/README [code] | Oil/water/surfactant interface |
| SW_FMT3_1D/README [code] | Square-well fluid near a hard wall |
| YUKAWA_FMT1_3D/README [code] | Yukawa fluid around a larger Yukawa sphere |