#============================================================#
# test torque around a pca axis                              #
#============================================================#
system echo = off
system verbose = false

# set units
units scale  name = mass   uname = reducedMass   value = 10000.0

# open pdb file
database open name = neck format = pdb  file = ../data/neck_xform.pdb

# read molecule
molecule read  name = m1   database = neck


# create some domains
domain create iq1 = AC[760-788]
domain iq1 backbone color = [ 1 0 0 ] width = 2 show
#domain iq1 atoms color = [ 1 0 0 ] show = true

domain create iq2 = BC[788-814]
domain iq2 backbone color = [ 0 1 0 ] width = 2 show
#domain iq2 bonds  atom_color = element  atoms = true show = true
#domain iq2 atoms color = [ 0 1 0 ] show = true

domain create iq3 = DC[814-836]
domain iq3 backbone color = [ 0 0 1 ] width = 2 show
#domain iq3 bonds  atom_color = element  atoms = true show = true
#domain iq3 atoms color = [ 0 0 1 ] show = true

domain create iq3C = C[814-836]
domain iq3C pca show=true 

domain create hc = C


#--------------------------------------------------------------#
#                      create bodies                           #
#--------------------------------------------------------------#
body create  name = ground    type = ground
body create  name = iq1_body  type = rigid   domain = iq1
body create  name = iq2_body  type = rigid   domain = iq2
body create  name = iq3_body  type = rigid   domain = iq3


#--------------------------------------------------------------#
#                 create a rigid simulation                    #
#--------------------------------------------------------------#

simulation create name = rsim  type = rigid

# add bodies
#-----------
simulation rsim add body = ground
simulation rsim add body = iq1_body
simulation rsim add body = iq2_body
simulation rsim add body = iq3_body


# set solver
#-----------
simulation rsim solver = ode
simulation rsim solver finite_rotation = on


# add force
#----------
force create  name = force1            \
              type = explicit          \
              global_frame = true      \
              torque = true            \
              use_pca = true           \
              pca_domain = iq3         \
              pca_res = C              \
              direction = 2            \
              magnitude = 1.0          \
              scale = 1.0

simulation rsim add force = force1    \
                    body = iq3_body   \
                    time = { 0 1000 }

# initialize simulation
#----------------------
simulation rsim initialize
simulation rsim time step = 0.005 
#simulation  state  save_frequency = 100


#graphics write format = jpeg name = i1
#graphics record format = jpeg name = i1  on = true