#============================================================#
#               test trace for rigid body simulation         #
#============================================================#

# 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


# 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


#--------------------------------------------------------------#
#                      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 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 }


#--------------------------------------------------------------#
#                 create a course-grained model                #
#--------------------------------------------------------------#

model create name = model_1

# add joints
#-----------
model model_1 add joint = 1
model model_1 add joint = 2
model model_1 add joint = 3

# add bodies
#-----------
model model_1 add body = iq1_body
model model_1 add body = iq2_body
model model_1 add body = iq3_body

#model model_1 joints msize = 0.5 show = true
#model model_1 bodies msize = 0.5 show = true


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

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

# 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 = [ 1 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 = [ 0 1 0 ]  \
              scale = 1.0

simulation rsim add force = force2    \
                    body = iq2_body   \
                    time = { 0 1000 }


# initialize simulation
#----------------------
simulation rsim initialize
simulation rsim time step = 0.02 

simulation rsim  add trace  name = trace1  \
           global_frame = true    \
           point = iq3:C[835]  \
           color = [ 1 0 1 ]  \
           body = iq3_body   show = true


# 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