| commit | author | age | ||
| a6b1b5 | 1 | ####### Vesicle definitions ########### |
| SP | 2 | # nshell is a number of divisions of dipyramid |
| e98482 | 3 | nshell=17 |
| e86357 | 4 | # dmax is the max. bond length (in units l_min) |
| 304510 | 5 | dmax=1.7 |
| ea1cce | 6 | # dmin_interspecies in the min. dist. between different vertex species (in units l_min) |
| fe24d2 | 7 | dmin_interspecies=1.2 |
| e86357 | 8 | # bending rigidity of the membrane (in units kT) |
| 2dcc65 | 9 | xk0=10.0 |
| e86357 | 10 | # max step size (in units l_min) |
| a6b1b5 | 11 | stepsize=0.15 |
| e86357 | 12 | |
| M | 13 | # Pressure calculations |
| 14 | # (pswitch=1: calc. p*dV energy contribution) | |
| 45c708 | 15 | pswitch = 0 |
| 2dcc65 | 16 | # pressure difference: p_inside - p_outside (in units kT/l_min^3): |
| e98482 | 17 | pressure=10.0 |
| a6b1b5 | 18 | |
| 267433 | 19 | #Constant volume constraint (0 disable constant volume, 1 enable wiht additional vertex move, 2 enable with epsvol) |
| 37791b | 20 | constvolswitch=0 |
| dd5aca | 21 | constvolprecision=1e-14 |
| 9166cb | 22 | |
| c0ae90 | 23 | #Constant area constraint (0 disable constant area, 2 enable constant area with epsarea) |
| 8db203 | 24 | constareaswitch=0 |
| 9166cb | 25 | |
| 624f81 | 26 | ####### Polymer (brush) definitions ########### |
| a2db52 | 27 | # npoly is a number of polymers attached to npoly distinct vertices on vesicle |
| 073d28 | 28 | npoly=0 |
| 48bb92 | 29 | # nmono is a number of monomers in each polymer |
| fc6f3e | 30 | nmono=10 |
| 48bb92 | 31 | # Spring constant between monomers of the polymer |
| M | 32 | k_spring=800 |
| e98482 | 33 | #set to 1 if half of the polymeres are inside the vesicle |
| SP | 34 | internal_poly=1 |
| a6b1b5 | 35 | |
| 624f81 | 36 | ####### Filament (inside the vesicle) definitions ########### |
| 58230a | 37 | # nfil is a number of filaments inside the vesicle |
| 8db203 | 38 | nfil=0 |
| 58230a | 39 | # nfono is a number of monomers in each filament |
| 8db203 | 40 | nfono=3 |
| b30f45 | 41 | # Persistence lenght of the filaments (in units l_min) |
| 5c64e2 | 42 | xi=100 |
| 58230a | 43 | |
| M | 44 | ####### Nucleus (inside the vesicle) ########### |
| 45 | # Radius of an impenetrable hard sphere inside the vesicle | |
| f06f5f | 46 | R_nucleus=0 |
| bfa6c4 | 47 | R_nucleusX=0 |
| SP | 48 | R_nucleusY=0 |
| 49 | R_nucleusZ=0 | |
| a6b1b5 | 50 | ####### Cell definitions ############ |
| SP | 51 | nxmax=60 |
| 52 | nymax=60 | |
| 53 | nzmax=60 | |
| 54 | ||
| 55 | ||
| 56 | ####### Program Control ############ | |
| d7a113 | 57 | #how many MC sweeps between subsequent records of states to disk |
| a5e543 | 58 | #200000 |
| 032273 | 59 | mcsweeps=2000 |
| d7a113 | 60 | #how many initial mcsweeps*inititer MC sweeps before recording to disk? |
| a5e543 | 61 | #2 |
| 514ebc | 62 | inititer=0 |
| d7a113 | 63 | #how many records do you want on the disk iteration are there in a run? |
| a5e543 | 64 | #10000 |
| M | 65 | iterations=100 |
| d7a113 | 66 | |
| a6b1b5 | 67 | |
| dc77e8 | 68 | ###### Spherical harmonics ########### |
| 5a3862 | 69 | # If 0 then spherical harmonics are not calculated at all. |
| c60a49 | 70 | spherical_harmonics_coefficients=21 |
| dc77e8 | 71 | |
| a6b1b5 | 72 | #shut up if we are using cluster!!! |
| SP | 73 | quiet=false |
| 5c64e2 | 74 | |
| SP | 75 | |
| f74313 | 76 | |
| SP | 77 | #what type of multiprocessing? (*none, smp, cluster, distributed, cuda, auto) |
| 78 | #currently only none makes sense. | |
| 79 | multiprocessing=none | |
| 80 | #how many cores are allowed to process in SMP? | |
| 81 | smp_cores=2 | |
| 82 | #how many nodes in cluster? | |
| 83 | cluster_nodes=50 | |
| 84 | #max number of processes in distributed (voluntary) environment | |
| 85 | distributed_processes=50 | |
| 86 | #cuda options??? | |
| e5858f | 87 | |
| SP | 88 | |
| 89 | #number of vertices with spontaneous curvature (integer) | |
| 250de4 | 90 | number_of_vertices_with_c0=100 |
| e6efc6 | 91 | #c0/2 is spontaneous curvature. c0 is used as (c1+c1-c0)^2 in energy term (float) |
| 032273 | 92 | c0=0.5 |
| SP | 93 | #energy of attraction of vertices with spontaneous curvature (float, positive value for attraction) |
| 250de4 | 94 | w=10.0 |
| SP | 95 | #direct force on vesicles with spontaneous curvature (float) |
| 96 | F=2.0 | |
| 514ebc | 97 | |
| SP | 98 | |
| 99 | ||
| 100 | #plane confinement | |
| 101 | plane_confinement_switch=1 | |
| 102 | #final plane distance (float in lmin) | |
| 103 | plane_d=15 | |
| 104 | #plane to vesicle repulsion force while closing | |
| 105 | plane_F=1000 | |
