Energies Module¶
Module
Description
Organizes diffent energy types. Add new interaction energies here.
All energies are assumed to be of the form E=cof*x where cof is some constant and x is some function that depends on the positions, types, and/or orientation of the monomers.
Quick access
Needed modules
precision
(dp()
,epsapprox()
,pi()
)
Types
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type
energies/
mc_energy
¶ Type fields: %
cof
[real] :: Energy coefficienet, e.g. chi, kap, …%
de
[real] :: Change in energy%
dx
[real] :: Change in x%
e
[real] :: Energy in units of kT%
ind_on
[integer] :: Time when to turn energy on%
ison
[logical] :: Is energy type currently on?%
name_str
[character(len=8)] :: Name for display%
parallel_temper
[logical]%
x
[real] :: Energy/cof, i.e. observable that energy depends on
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type
Variables
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energies/
bend_
[integer,public/parameter/optional/default=6]¶ Bending constant
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energies/
bind_
[integer,public/parameter/optional/default=13]¶ Binding energy
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energies/
chi_
[integer,public/parameter/optional/default=1]¶ Flory-Huggins chi parameter
-
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energies/
confine_
[integer,public/parameter/optional/default=16]¶ Confinement energy
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energies/
couple_
[integer,public/parameter/optional/default=4]¶ Coupling constant (e.g. HP1 oligomerization)
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energies/
explicitbinding_
[integer,public/parameter/optional/default=15]¶ Explicit Binding energy (e.g. LEFs)
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energies/
external_
[integer,public/parameter/optional/default=10]¶ External potentail strength
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energies/
field_
[integer,public/parameter/optional/default=3]¶ Applied field
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energies/
global_twistliner_
[integer,public/parameter/optional/default=19]¶ Global twist linear portion
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energies/
global_twistquadratic_
[integer,public/parameter/optional/default=20]¶ Global twist quadratic portion
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energies/
internucleosome_
[integer,public/parameter/optional/default=22]¶ Internucleosomal potential
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energies/
kap_
[integer,public/parameter/optional/default=5]¶ Incompresability parameter
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energies/
maiersaupe_
[integer,public/parameter/optional/default=9]¶ Maier Saupe liquic crystal intercation
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energies/
mu_
[integer,public/parameter/optional/default=2]¶ Chemical potential (e.g. of HP1)
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energies/
number_of_energy_types
[integer,public/parameter/optional/default=22]¶
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energies/
self_
[integer,public/parameter/optional/default=14]¶ Self interaction energy
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energies/
shear_
[integer,public/parameter/optional/default=8]¶ Shear constant
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energies/
sterics_
[integer,public/parameter/optional/default=21]¶ Steric collision energy when using GJK
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energies/
stretch_
[integer,public/parameter/optional/default=7]¶ Stretch constant
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energies/
twist_
[integer,public/parameter/optional/default=12]¶ Twist constant
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energies/
twobody_
[integer,public/parameter/optional/default=11]¶ Two body interaction strength
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energies/
umbrella_
[integer,public/parameter/optional/default=17]¶ Energy from umbrella sampling (linear partion)
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energies/
umbrellaquadratic_
[integer,public/parameter/optional/default=18]¶ Quadratic energy from umbrella
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Subroutines and functions
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subroutine
energies/
set_up_energyof
()¶ Set up energy module.
Called from: set_param_defaults()
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subroutine
energies/
set_all_energy_to_zero
()¶ Reset all dE, E, x, and dx values to zero.
Called from: initialize_wlcsim_data()
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subroutine
energies/
set_all_denergy_to_zero
()¶ Set all dE and dx values to zero
Called from: mcsim()
,calculate_energies_from_scratch()
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subroutine
energies/
sum_all_denergies
(total_energy)¶ Sums total change in energy.
Parameters: total_energy [real,out] Called from: mcsim()
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subroutine
energies/
accept_all_energies
()¶ Set E to E+dE because move has been accepted
Called from: mcsim()
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subroutine
energies/
calc_all_de_from_dx
()¶ dE=cof*dx
Called from: mcsim()
,calculate_energies_from_scratch()
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subroutine
energies/
apply_energy_ison
()¶ Zero energies that are off.
Called from: mcsim()
,calculate_energies_from_scratch()
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subroutine
energies/
print_all_denergies
()¶ Print energie changes to standard out