#============================================================*
#               test rigid body simulation                   *
#============================================================*

# read molecule
molecule read name = m1 format = pdb file = iq.pdb

# 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      type = rigid   domain = iq1
body create  name = iq2      type = rigid   domain = iq2


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

joint create            \
      name = 1          \
      type = universal  \
      domain = iq1      \
      axis1 = [ 0 1 0 ] \
      axis2 = [ 1 0 0 ] \
      res = C762        \
      use = CA

joint 1 color = [ 1 0 0 ] msize = 0.1 shading = color show = true 
joint 1 bodies = { ground iq1 }

joint create            \
      name = 2          \
      type = pin        \
      axis = [ 0 1 0 ]  \
      domain = iq1      \
      res = C788        \
      use = CA

joint 2 color = [ 0 1 0 ] msize = 0.1 shading = flat display = line show = true 
joint 2 bodies = { iq1 iq2 }


#--------------------------------------------------------------#
#                 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
model model_1 add body = iq2

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
simulation rsim add body = iq2    
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             

simulation rsim initialize