#============================================================*
#               test 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[762-788]
domain iq1 backbone color = [ 1 0 0 ] width = 2 show
domain create iq2 = BC[788-813]
domain iq2 backbone color = [ 0 1 0 ] width = 2 show


#--------------------------------------------------------------#
#                      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 = surf1    type = rigid   surface = iq1surf


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

joint create            \
      name = 1          \
      type = ball       \
      domain = iq1      \
      res = C[762]       \
      use = CA

joint 1 color = [ 1 0 0 ] msize = 0.1 shading = color show = true 
joint 1 bodies = { ground iq1_body }

joint create            \
      name = 2          \
      type = ball       \
      domain = iq1      \
      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 }


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

model create name = model_1

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

# add bodies
model model_1 add body = iq1_body
model model_1 add body = iq2_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 = iq1_body
simulation rsim add body = iq2_body
simulation rsim add body = ground 

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

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


# add forces
#-----------
force create  name = force1         \
              type = explicit         \
              point = [ 10 10 0 ]    \
              direction = [ 1 0 0 ]  \
              scale = 0.1

simulation rsim add force = force1    \
                    body = iq1_body   \
                    time = { 0 1000 }


# initialize simulation
#----------------------
simulation rsim initialize 


# step simulation
#----------------
simulation rsim step 
#simulation rsim step 
#simulation rsim step 
#simulation rsim step