| | |
|---|
| | | ####### Vesicle definitions ########### |
|---|
| | | # nshell is a number of divisions of dipyramid |
|---|
| | | nshell=17 |
|---|
| | | nshell=7 |
|---|
| | | # dmax is the max. bond length (in units l_min) |
|---|
| | | dmax=1.7 |
|---|
| | | # dmin_interspecies in the min. dist. between different vertex species (in units l_min) |
|---|
| | |
|---|
| | | #Constant area constraint (0 disable constant area, 2 enable constant area with epsarea) |
|---|
| | | constareaswitch=0 |
|---|
| | | |
|---|
| | | |
|---|
| | | #Stretching |
|---|
| | | stretchswitch=0 |
|---|
| | | xkA0=1.0 |
|---|
| | | |
|---|
| | | ####### Polymer (brush) definitions ########### |
|---|
| | | # npoly is a number of polymers attached to npoly distinct vertices on vesicle |
|---|
| | | npoly=800 |
|---|
| | | npoly=0 |
|---|
| | | # nmono is a number of monomers in each polymer |
|---|
| | | nmono=6 |
|---|
| | | nmono=0 |
|---|
| | | # Spring constant between monomers of the polymer |
|---|
| | | k_spring=800 |
|---|
| | | #set to 1 if half of the polymeres are inside the vesicle |
|---|
| | | internal_poly=1 |
|---|
| | | internal_poly=0 |
|---|
| | | |
|---|
| | | ####### Filament (inside the vesicle) definitions ########### |
|---|
| | | # nfil is a number of filaments inside the vesicle |
|---|
| | |
|---|
| | | R_nucleusY=0 |
|---|
| | | R_nucleusZ=0 |
|---|
| | | ####### Cell definitions ############ |
|---|
| | | nxmax=60 |
|---|
| | | nymax=60 |
|---|
| | | nzmax=60 |
|---|
| | | nxmax=100 |
|---|
| | | nymax=100 |
|---|
| | | nzmax=100 |
|---|
| | | |
|---|
| | | |
|---|
| | | ####### Program Control ############ |
|---|
| | | #how many MC sweeps between subsequent records of states to disk |
|---|
| | | #200000 |
|---|
| | | mcsweeps=2000 |
|---|
| | | mcsweeps=200 |
|---|
| | | #how many initial mcsweeps*inititer MC sweeps before recording to disk? |
|---|
| | | #2 |
|---|
| | | inititer=10 |
|---|
| | | inititer=0 |
|---|
| | | #how many records do you want on the disk iteration are there in a run? |
|---|
| | | #10000 |
|---|
| | | iterations=100 |
|---|
| | | iterations=10 |
|---|
| | | |
|---|
| | | |
|---|
| | | ###### Spherical harmonics ########### |
|---|
| | |
|---|
| | | #cuda options??? |
|---|
| | | |
|---|
| | | |
|---|
| | | #NirGov branch only! |
|---|
| | | #number of vertices with spontaneous curvature (integer) |
|---|
| | | number_of_vertices_with_c0=100 |
|---|
| | | #spontaneous curvature (float) |
|---|
| | | c0=0.5 |
|---|
| | | number_of_vertices_with_c0=200 |
|---|
| | | #c0/2 is spontaneous curvature. c0 is used as (c1+c1-c0)^2 in energy term (float) |
|---|
| | | c0=1.0 |
|---|
| | | #energy of attraction of vertices with spontaneous curvature (float, positive value for attraction) |
|---|
| | | w=10.0 |
|---|
| | | #direct force on vesicles with spontaneous curvature (float) |
|---|
| | | F=2.0 |
|---|
| | | |
|---|
| | | |
|---|
| | | |
|---|
| | | #plane confinement |
|---|
| | | plane_confinement_switch=0 |
|---|
| | | #final plane distance (float in lmin) |
|---|
| | | plane_d=10 |
|---|
| | | #plane to vesicle repulsion force while closing |
|---|
| | | plane_F=10 |
|---|
