if(MD_PACKAGE == "langevin"):
from lib.langevin_module import MD_module
md_module = MD_module(CONFIGFILE, DEBUG)
if(MD_PACKAGE == "gromacs"):
print("Sorry, support for gromacs is not implemented yet.")
sys.exit(-1)
# Initiate the reweighter
if REWEIGHTING_RANGE > 0:
reweighter = reweighting.Reweighting( reweighting_range = REWEIGHTING_RANGE )
# Initiate iterations
if APPEND == True:
# load the last two iterations if existing for proper function of
# cleanup module
if logger.getLastIterationId() > 1:
iterations = logger.loadLastIterations(N=2)
else:
logger.loadLastIterations(N=1)
# Load the previous iterations to restore the rate matrices for the reweighter module
if REWEIGHTING_RANGE > 0 and iterations[-1].getId() <= REWEIGHTING_MAX_ITERATION:
print('Loading previous iterations to restore rate matrix for reweighting...')
for iteration_counter_tmp in range(1,iterations[-1].getId() + 1):
iteration_tmp = logger.loadIteration(iteration_counter_tmp)
reweighter.storeRateMatrix(iteration_tmp)
iteration_tmp = []
if APPEND_NEW_CONFIG:
iterations[-1].boundaries = INITIAL_BOUNDARIES
iterations[-1].sample_region = INITIAL_SAMPLE_REGION
iterations[-1].target_number_of_segments = INITIAL_TARGET_NUMBER_OF_SEGMENTS
help="Segment MD propagation time tau used in hdWE simulations.")
parser.add_argument(
'-p',
'--plot',
dest="plot",
required=False,
default=False,
action="store_true",
help="Plot probabilities from start state per bin and iteration")
# Initialize
args = parser.parse_args()
first_iteration = 0
last_iteration = args.last_iteration
logger = Logger(args.logdir)
if last_iteration < 0:
last_iteration = logger.getLastIterationId()
# get the bin Ids of start state and target state
start_state = args.start_state
target_state = args.target_state
last_iteration_tmp = logger.loadIteration(last_iteration)
found_target_state = False
for this_bin in last_iteration_tmp.bins:
if all(this_bin.getCoordinateIds() == start_state):
start_state_id = this_bin.getId()
if all(this_bin.getCoordinateIds() == target_state):
target_state_id = this_bin.getId()
found_target_state = True
if found_target_state == False:
target_state_id = 1e99
print('Warning: Target state not found in given iterations')
help="Output filename")
parser.add_argument("--probability",
dest="probability",
action="store_true",
default=False)
# Initialize
print(
'\033[1mCalculating Bin Free Energies\033[0m (Free Energy is given in kcal/mol at 298K).'
)
args = parser.parse_args()
last_iteration = args.last_iteration
first_iteration = args.first_iteration
logger = Logger(args.logdir)
if last_iteration < 0:
last_iteration = logger.getLastIterationId()
n_iterations = last_iteration - first_iteration + 1
#initialize bin probability evolution array with size of last frame number_of_bins
iteration = logger.loadIterations(logger.getLastIterationId(),
logger.getLastIterationId())[0]
n_bins = iteration.getNumberOfBins()
bin_probabilities = numpy.zeros(
[n_iterations, iteration.getNumberOfBins(), 2], float)
for i in range(0, len(bin_probabilities[:, 0, 0])):
for j in range(0, len(bin_probabilities[0, :, 0])):
for k in range(0, 2):
bin_probabilities[i, j, k] = 0
for i in range(first_iteration, last_iteration):
