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
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