#============================================================*
#               test position  measurement                   *
#============================================================*

system echo = off
system verbose = false

# 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 = [ 0.2 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 0.5 0 ]  \
              scale = 1.0

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


# add a measurement 
#------------------

#--- 1 ---

measurement  create  name = pos1   type = position \
             point  = iq3:C[835]   body = iq3_body 

simulation rsim add measurement = pos1 
simulation rsim  write  measurement = pos1  file_name = pos1



# initialize simulation
#----------------------
simulation rsim initialize
simulation rsim time step = 0.02 
#simulation  state  save_frequency = 100


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