#============================================================*
#               test rigid body simulation                   *
#                                                            *
# look at difference in dynamics with translated model.      *
#============================================================*

# set units
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
molecule m1  xform  translation = [ 10 0 0 ] 


# create a 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 hc = C



# open pdb file
database open name = neck2 format = pdb  file = ../../data/neck_xform.pdb

# read molecule
molecule read  name = m2   database = neck2


# create a some domains
domain create iq1a = AC[760-788]
domain iq1a backbone color = [ 0.5 0 0 ] width = 2 show

domain create iq2a = BC[788-814]
domain iq2a backbone color = [ 0 0.5 0 ] width = 2 show

domain create iq3a = DC[814-836]
domain iq3a backbone color = [ 0 0 0.5 ] width = 2 show

domain create hca = 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

body create  name = iq1a_body  type = rigid   domain = iq1a
body create  name = iq2a_body  type = rigid   domain = iq2a
body create  name = iq3a_body  type = rigid   domain = iq3a

#--------------------------------------------------------------#
#                      create joints                           #
#--------------------------------------------------------------#

# joint 1
#--------
joint create   name = 1    type = ball   domain = iq1    res = C[760]  use = CA
joint 1 color = [ 1 0 0 ] msize = 0.1 shading = color show = true 
joint 1 bodies = { ground iq1_body }

# joint 2
#--------
joint create  name = 2    type = ball  domain = hc  res = C[788]  use = CA
joint 2 color = [ 0 1 0 ] msize = 0.1 shading = flat display = line show = true 
joint 2 bodies = { iq1_body iq2_body }

# joint 3
#--------
joint create   name = 3   type = ball   domain = hc   res = C[814]   use = CA
joint 3 color = [ 0 0 1 ] msize = 0.1 shading = flat display = line show = true
joint 3 bodies = { iq2_body iq3_body }


# joint 1
#--------
joint create   name = 1a   type = ball   domain = iq1a    res = C[760]  use = CA
joint 1a color = [ 1 0 0 ] msize = 0.1 shading = color show = true
joint 1a bodies = { ground iq1a_body }

# joint 2
#--------
joint create  name = 2a    type = ball  domain = hca  res = C[788]  use = CA
joint 2a color = [ 0 1 0 ] msize = 0.1 shading = flat display = line show = true
joint 2a bodies = { iq1a_body iq2a_body }

# joint 3
#--------
joint create   name = 3a   type = ball   domain = hca   res = C[814]   use = CA
joint 3a color = [ 0 0 1 ] msize = 0.1 shading = flat display = line show = true
joint 3a bodies = { iq2a_body iq3a_body }

#--------------------------------------------------------------#
#                 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

simulation rsim add body = iq1a_body
simulation rsim add body = iq2a_body
simulation rsim add body = iq3a_body

# add joints
#-----------
simulation rsim add joint = 1
simulation rsim add joint = 2
simulation rsim add joint = 3

simulation rsim add joint = 1a
simulation rsim add joint = 2a
simulation rsim add joint = 3a

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


# add forces
#-----------
force create  name = force1         \
              type = explicit         \
              point = [ 0 0 0 ]    \
              direction = [ 40 0 0 ]  \
              scale = 1.0

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


force create  name = force2         \
              type = explicit         \
              point = [ 0 0 0 ]    \
              direction = [ 40 0 0 ]  \
              scale = 1.0

simulation rsim add force = force2    \
                    body = iq3a_body   \
                    time = { 0 1000 }


# initialize simulation
#----------------------
simulation rsim initialize
simulation rsim time step = 0.001 
simulation rsim momentum = on

simulation rsim add trace name = tr1   \
                body = iq3_body        \
                color = [ 1 0 0 ]      \
                global_frame = false   \
                point = [ 0 0 0 ]

simulation rsim add trace name = tr1a   \
                body = iq3a_body        \
                color = [ 1 1 1 ]      \
                global_frame = false   \
                point = [ 0 0 0 ]


# step simulation
#----------------
#simulation rsim step = 100
#simulation rsim step
#simulation rsim step
#simulation rsim step

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