From b38ffa62aaea143b1b563451e1b921883d257947 Mon Sep 17 00:00:00 2001
From: Thomas OBrien <obrien@lorentz.leidenuniv.nl>
Date: Wed, 24 Oct 2018 23:13:12 +0200
Subject: [PATCH 1/5] Added option to auto-shrink waiting gates to only include
 the time taken by actual gates, this way circuits can be tetrised. Also
 stopped builder from splitting setup into component pieces upon
 initialisation

---
 qsoverlay/DiCarlo_setup.py     |   9 +-
 qsoverlay/circuit_builder.py   | 158 +++++++++++++++++++--------------
 qsoverlay/experiment_setup.py  |   8 +-
 qsoverlay/test/test_builder.py |  60 ++++++++++---
 4 files changed, 155 insertions(+), 80 deletions(-)

diff --git a/qsoverlay/DiCarlo_setup.py b/qsoverlay/DiCarlo_setup.py
index 526c5b9..7dff27e 100644
--- a/qsoverlay/DiCarlo_setup.py
+++ b/qsoverlay/DiCarlo_setup.py
@@ -134,7 +134,14 @@ def quick_setup(qubit_list, connectivity_dic=None, rng=None, *, seed=None,
     setup['gate_set'] = make_1q2q_gateset(qubit_dic=setup['qubit_dic'],
                                           gate_dic=setup['gate_dic'],
                                           connectivity_dic=connectivity_dic)
-    return Setup(**setup)
+
+    system_params = {
+        'uses_waiting_gates': True
+    }
+
+    setup = Setup(**setup, system_params=system_params)
+
+    return setup
 
 
 def asymmetric_setup(qubit_parameters=None,
diff --git a/qsoverlay/circuit_builder.py b/qsoverlay/circuit_builder.py
index a02f534..74ae258 100644
--- a/qsoverlay/circuit_builder.py
+++ b/qsoverlay/circuit_builder.py
@@ -16,45 +16,17 @@
 
 class Builder:
 
-    def __init__(self,
-                 setup=None,
-                 qubit_dic=None,
-                 gate_dic=None,
-                 gate_set=None,
-                 update_rules=None,
-                 **kwargs):
+    def __init__(self, setup, **kwargs):
         '''
-        qubit_dic: list of the qubits in the system.
-            Each qubit should have a set of parameters,
-            which is called whenever required by the gates.
-        gate_dic: a dictionary of allowed gates.
-            Each 'allowed gate' consists of:
-                - the function to be called
-                - a set of 'qubit_args' that will be found in
-                    the qubit dictionary and passed to the gate.
-                - a 'time' - the length of the gate
-            Note that 'Measure' should be in the gate_set
-        gate_set: a dictionary of allowed gate instances.
-            An allowed gate instance is a list of the gate
-            along with the qubits it is performed between.
-        update_rules: a set of rules for updating the system.
-            (i.e. between experiments).
+        Args:
+        -------
+        setup: an experiment_setup.Setup containing details of
+            the experiment.
 
         kwargs: Can add t1 and t2 via the kwargs instead of
             passing them with the qubit_dic.
         '''
-        if setup is not None:
-            self.qubit_dic = setup.qubit_dic
-            self.gate_dic = setup.gate_dic
-            self.gate_set = setup.gate_set
-            self.update_rules = setup.update_rules
-        else:
-            self.qubit_dic = qubit_dic or {}
-            self.gate_dic = gate_dic or {}
-            self.gate_set = gate_set or {}
-            self.update_rules = update_rules or []
-
-        self.save_flag = True
+        self.setup = setup
         self.new_circuit(**kwargs)
 
     def new_circuit(self, circuit_title='New Circuit', **kwargs):
@@ -70,9 +42,14 @@ def new_circuit(self, circuit_title='New Circuit', **kwargs):
 
         # Times stores the current time of every qubit (beginning at 0)
         self.times = {}
+        self.tmins = {}
+
+        # save_flag is used to keep track of which gates have been
+        # saved during a circuit, and needs to be reset here.
+        self.save_flag = True
 
         # Make qubits
-        for qubit, qubit_args in sorted(self.qubit_dic.items()):
+        for qubit, qubit_args in sorted(self.setup.qubit_dic.items()):
 
             if 'classical' in qubit_args.keys() and\
                     qubit_args['classical'] is True:
@@ -95,6 +72,7 @@ def new_circuit(self, circuit_title='New Circuit', **kwargs):
 
             # Initialise the time of the latest gate on each qubit to 0
             self.times[qubit] = 0
+            self.tmins[qubit] = None
 
     def make_reverse_circuit(self, title='reversed',
                              finalize=True):
@@ -111,8 +89,8 @@ def make_reverse_circuit(self, title='reversed',
         for n, gate_desc in enumerate(reversed_circuit_list):
             gate_name = gate_desc[0]
 
-            num_qubits = self.gate_dic[gate_name]['num_qubits']
-            user_kws = self.gate_dic[gate_name]['user_kws']
+            num_qubits = self.setup.gate_dic[gate_name]['num_qubits']
+            user_kws = self.setup.gate_dic[gate_name]['user_kws']
 
             if 'angle' in user_kws:
                 gate_desc = list(gate_desc)
@@ -120,10 +98,7 @@ def make_reverse_circuit(self, title='reversed',
                 gate_desc[num_qubits + 1 + angle_index] *= -1
                 reversed_circuit_list[n] = tuple(gate_desc)
 
-        reversed_circuit_builder = Builder(qubit_dic=self.qubit_dic,
-                                           gate_dic=self.gate_dic,
-                                           gate_set=self.gate_set,
-                                           update_rules=self.update_rules)
+        reversed_circuit_builder = Builder(setup=self.setup)
         reversed_circuit_builder.add_circuit_list(reversed_circuit_list)
         if finalize:
             reversed_circuit_builder.finalize()
@@ -153,8 +128,8 @@ def add_qasm(self, qasm_generator, qubits_first=True, **params):
             # Get the gate name
             gate_name = line[:spaces[0]]
 
-            num_qubits = self.gate_dic[gate_name]['num_qubits']
-            user_kws = self.gate_dic[gate_name]['user_kws']
+            num_qubits = self.setup.gate_dic[gate_name]['num_qubits']
+            user_kws = self.setup.gate_dic[gate_name]['user_kws']
 
             if gate_name == 'measure':
                 # line looks like 'measure q -> c;'
@@ -224,8 +199,8 @@ def add_circuit_list(self, circuit_list):
     def __lt__(self, gate_desc):
         gate_name = gate_desc[0]
 
-        num_qubits = self.gate_dic[gate_name]['num_qubits']
-        user_kws = self.gate_dic[gate_name]['user_kws']
+        num_qubits = self.setup.gate_dic[gate_name]['num_qubits']
+        user_kws = self.setup.gate_dic[gate_name]['user_kws']
 
         if len(gate_desc) == len(user_kws) + num_qubits + 2:
             return_flag = gate_desc[-1]
@@ -264,7 +239,7 @@ def add_gate(self, gate_name,
         # the same for every qubit/pair of qubits).
         gate_tuple = (gate_name, *qubit_list)
 
-        circuit_args, builder_args = self.gate_set[gate_tuple]
+        circuit_args, builder_args = self.setup.gate_set[gate_tuple]
 
         # kwargs is the list of arguments that gets passed to the gate
         # itself. We initiate with the set of additional arguments passed
@@ -302,7 +277,7 @@ def add_gate(self, gate_name,
         # data.
         if self.save_flag:
             user_data = [kwargs[kw]
-                         for kw in self.gate_dic[gate_name]['user_kws']]
+                         for kw in self.setup.gate_dic[gate_name]['user_kws']]
             if return_flag is not False:
                 self.circuit_list.append((gate_name, *qubit_list,
                                           *user_data, return_flag))
@@ -311,7 +286,7 @@ def add_gate(self, gate_name,
                                           *user_data))
 
         # Get the gate to add to quantumsim.
-        gate = self.gate_dic[gate_name]['function']
+        gate = self.setup.gate_dic[gate_name]['function']
 
         # The save flag prevents saving multiple gate
         # definitions when using recursive gates (i.e.
@@ -344,6 +319,11 @@ def add_gate(self, gate_name,
         for qubit in qubit_list:
             self.times[qubit] = max(self.times[qubit], time + gate_time)
 
+            # If this qubit has not been used before, store the start
+            # of this gate as the first time it is activated.
+            if self.tmins[qubit] is None:
+                self.tmins[qubit] = time
+
         # My current best idea for adjustable gates - return the
         # gate that could be adjusted to the user.
         if return_flag is not False:
@@ -353,22 +333,75 @@ def update(self, **kwargs):
         for rule in self.update_rules:
             update_function_dic[rule](self, **kwargs)
 
-    def finalize(self, topo_order=False, t_add=0):
+    def finalize(self, topo_order=False, dtmax=0, dtmin=0, shrink=False):
+        """
+        Script to run to finalize gates. Currently adds waiting gates
+        as required and sorts gates.
+
+        Args:
+        --------
+        topo_order : bool
+            whether to toposort gates or simply order them by time.
+        dtmax : float or dict of floats
+            time to pad qubits by (i.e. dead time after the gates 
+            in the circuit are executed). If float, applies same
+            padding to all qubits.
+        dtmin : float or dict of floats
+            time to pad qubits by on the left (i.e. dead time before
+            any gates are executed). If float, applies same padding
+            to all qubits.
+        shrink : bool
+            whether to shrink resting gates around qubits. When
         """
-        Adds resting gates to all systems as required.
-        quantumsim currently assumes fixed values for photon
-        numbers, so we take them from a random qubit
 
-        Photons in quantumsim are currently broken, so
-        they're not in here right now.
+        if self.setup.system_params['uses_waiting_gates'] is True:
+            self.add_waiting_gates(
+                dtmin=dtmin, dtmax=dtmax, shrink=shrink)
+
+        if topo_order is True:
+            self.circuit.order()
+        else:
+            self.circuit.gates = sorted(self.circuit.gates,
+                                        key=lambda x: x.time)
+
+    def add_waiting_gates(self, dtmin=0, dtmax=0, shrink=False):
         """
+        Function to add waiting gates to system
+
+        Args:
+        --------
+        dtmax : float or dict of floats
+            time to pad qubits by (i.e. dead time after the gates 
+            in the circuit are executed). If float, applies same
+            padding to all qubits.
+        dtmin : float or dict of floats
+            time to pad qubits by on the left (i.e. dead time before
+            any gates are executed). If float, applies same padding
+            to all qubits.
+        shrink : bool
+            whether to shrink resting gates around qubits. When
+        """
+        if shrink:
+            tmin = self.tmins
+            tmax = self.times
+        else:
+            circuit_time = max(self.times.values())
+            tmax = {key: circuit_time for key in self.times.keys()}
+            tmin = {key: 0 for key in self.times.keys()}
+
+        if type(dtmax) == dict:
+            for key,val in dtmax.items():
+                tmax[key] += val
+        else:
+            for key in tmax.keys():
+                tmax[key] += dtmax
 
-        circuit_time = max(self.times.values())
-        if type(t_add) == dict:
-            circuit_time = {key: val + circuit_time
-                            for key, val in t_add.items()}
+        if type(dtmin) == dict:
+            for key,val in dtmin.items():
+                tmin[key] -= val
         else:
-            circuit_time += t_add
+            for key in tmin.keys():
+                tmin[key] -= dtmin
 
         # args = list(self.qubit_dic.values())[0]
 
@@ -380,9 +413,4 @@ def finalize(self, topo_order=False, t_add=0):
         #         chi=args['chi'])
         # else:
 
-        self.circuit.add_waiting_gates(tmin=0, tmax=circuit_time)
-        if topo_order is True:
-            self.circuit.order()
-        else:
-            self.circuit.gates = sorted(self.circuit.gates,
-                                        key=lambda x: x.time)
+        self.circuit.add_waiting_gates(tmin=tmin, tmax=tmax)
diff --git a/qsoverlay/experiment_setup.py b/qsoverlay/experiment_setup.py
index 8adbe37..27e07a4 100644
--- a/qsoverlay/experiment_setup.py
+++ b/qsoverlay/experiment_setup.py
@@ -15,7 +15,8 @@ def __init__(
             self, filename=None,
             seed=None, state=None,
             gate_dic=None, update_rules=None,
-            qubit_dic=None, gate_set=None):
+            qubit_dic=None, gate_set=None,
+            system_params=None):
 
         if filename is not None:
             self.load(filename, seed, state)
@@ -24,6 +25,7 @@ def __init__(
             self.update_rules = update_rules or []
             self.qubit_dic = qubit_dic or {}
             self.gate_set = gate_set or {}
+            self.system_params = system_params or {}
 
     def load(self, filename, seed=None, state=None):
         with open(filename, 'r') as infile:
@@ -31,6 +33,7 @@ def load(self, filename, seed=None, state=None):
 
         self.update_rules = setup_load_format['update_rules']
         self.qubit_dic = setup_load_format['qubit_dic']
+        self.system_params = setup_load_format['system_params']
 
         # Currently assumes each qubit uses the same
         # uniform_noisy_sampler - this needs fixing
@@ -90,7 +93,8 @@ def save(self, filename):
             'gate_dic': gate_dic_save_format,
             'update_rules': self.update_rules,
             'qubit_dic': qubit_dic_save_format,
-            'gate_set': gate_set_save_format
+            'gate_set': gate_set_save_format,
+            'system_params': system_params
         }
         with open(filename, 'w') as outfile:
             json.dump(setup_save_format, outfile)
diff --git a/qsoverlay/test/test_builder.py b/qsoverlay/test/test_builder.py
index a2520ca..3dc552d 100644
--- a/qsoverlay/test/test_builder.py
+++ b/qsoverlay/test/test_builder.py
@@ -1,4 +1,5 @@
 from qsoverlay.circuit_builder import Builder
+from qsoverlay.experiment_setup import Setup
 from qsoverlay.DiCarlo_setup import quick_setup
 from quantumsim.sparsedm import SparseDM
 import pytest
@@ -12,13 +13,14 @@ def test_init(self):
         qubit_dic = {'q_test': {}}
         gate_dic = {}
         gate_set = {}
-        b = Builder(qubit_dic=qubit_dic,
-                    gate_dic=gate_dic,
-                    gate_set=gate_set,
+        setup = Setup(qubit_dic=qubit_dic,
+                      gate_dic=gate_dic,
+                      gate_set=gate_set)
+        b = Builder(setup=setup,
                     circuit_title='Test')
-        assert len(b.qubit_dic.keys()) == 1
-        assert b.gate_dic == {}
-        assert b.gate_set == {}
+        assert len(b.setup.qubit_dic.keys()) == 1
+        assert b.setup.gate_dic == {}
+        assert b.setup.gate_set == {}
         assert len(b.times.keys()) == 1
         assert b.circuit.title == 'Test'
         assert len(b.circuit.qubits) == 1
@@ -31,9 +33,10 @@ def test_T1T2(self):
         qubit_dic = {'q_test': {'t1': 10, 't2': 20}}
         gate_dic = {}
         gate_set = {}
-        b = Builder(qubit_dic=qubit_dic,
-                    gate_dic=gate_dic,
-                    gate_set=gate_set,
+        setup = Setup(qubit_dic=qubit_dic,
+                      gate_dic=gate_dic,
+                      gate_set=gate_set)
+        b = Builder(setup=setup,
                     circuit_title='Test')
         assert b.circuit.qubits[0].t1 == 10
         assert b.circuit.qubits[0].t2 == 20
@@ -42,9 +45,10 @@ def test_T1T2_kwarginit(self):
         qubit_dic = {'q_test': {}}
         gate_dic = {}
         gate_set = {}
-        b = Builder(qubit_dic=qubit_dic,
-                    gate_dic=gate_dic,
-                    gate_set=gate_set,
+        setup = Setup(qubit_dic=qubit_dic,
+                      gate_dic=gate_dic,
+                      gate_set=gate_set)
+        b = Builder(setup=setup,
                     circuit_title='Test',
                     t1=20,
                     t2=30)
@@ -140,3 +144,35 @@ def test_make_imperfect_bell(self):
         assert np.abs(diag[3]-0.5) < 1e-2
         assert np.abs(diag[1]) < 3e-2
         assert np.abs(diag[2]) < 3e-2
+
+    def test_shrink(self):
+        qubit_list = ['q0','q1']
+        with pytest.warns(UserWarning):
+            setup = quick_setup(qubit_list)
+        sq_gate_time = setup.qubit_dic['q0']['oneq_gate_time']
+        cp_gate_time = setup.qubit_dic['q0']['CZ_gate_time']
+        b = Builder(setup)
+        b.add_gate('RotateY', ['q0'], angle=np.pi/2)
+        b.add_gate('CZ', ['q0', 'q1'])
+        b.add_gate('RotateY', ['q1'], angle=-np.pi/2)
+        b.finalize(shrink=True)
+        assert min([gate.time for gate in b.circuit.gates
+                    if 'q1' in gate.involved_qubits]) == sq_gate_time + cp_gate_time/4
+        assert max([gate.time for gate in b.circuit.gates
+                    if 'q0' in gate.involved_qubits]) == sq_gate_time + 3*cp_gate_time/4
+
+    def test_noshrink(self):
+        qubit_list = ['q0','q1']
+        with pytest.warns(UserWarning):
+            setup = quick_setup(qubit_list)
+        sq_gate_time = setup.qubit_dic['q0']['oneq_gate_time']
+        cp_gate_time = setup.qubit_dic['q0']['CZ_gate_time']
+        b = Builder(setup)
+        b.add_gate('RotateY', ['q0'], angle=np.pi/2)
+        b.add_gate('CZ', ['q0', 'q1'])
+        b.add_gate('RotateY', ['q1'], angle=-np.pi/2)
+        b.finalize(shrink=False)
+        assert min([gate.time for gate in b.circuit.gates
+                    if 'q1' in gate.involved_qubits]) == sq_gate_time/2 + cp_gate_time/4
+        assert max([gate.time for gate in b.circuit.gates
+                    if 'q0' in gate.involved_qubits]) == sq_gate_time*3/2 + cp_gate_time*3/4

From 9dcb180ae0333fef0efb3ea311b703638de511f3 Mon Sep 17 00:00:00 2001
From: Thomas OBrien <obrien@lorentz.leidenuniv.nl>
Date: Thu, 1 Nov 2018 16:01:20 +0100
Subject: [PATCH 2/5] Changed times slightly

---
 qsoverlay/circuit_builder.py | 35 ++++++++++++++++++++++++-----------
 1 file changed, 24 insertions(+), 11 deletions(-)

diff --git a/qsoverlay/circuit_builder.py b/qsoverlay/circuit_builder.py
index f86214e..63344f8 100644
--- a/qsoverlay/circuit_builder.py
+++ b/qsoverlay/circuit_builder.py
@@ -226,10 +226,10 @@ def add_gates_simultaneous(self, gate_descriptions):
         starting_time = max([
             self.times[gate_desc[j]]
             for gate_desc in gate_descriptions
-            for j in range(1, self.gate_dic[gate_desc[0]]['num_qubits']+1)])
+            for j in range(1, self.setup.gate_dic[gate_desc[0]]['num_qubits']+1)])
 
         for gate_desc in gate_descriptions:
-            num_qubits = self.gate_dic[gate_desc[0]]['num_qubits']
+            num_qubits = self.setup.gate_dic[gate_desc[0]]['num_qubits']
             qubit_list = gate_desc[1:num_qubits + 1]
             for qubit in qubit_list:
                 self.times[qubit] = starting_time
@@ -361,7 +361,8 @@ def update(self, **kwargs):
         for rule in self.update_rules:
             update_function_dic[rule](self, **kwargs)
 
-    def finalize(self, topo_order=False, dtmax=0, dtmin=0, shrink=False):
+    def finalize(self, topo_order=False, tmin=None, tmax=None,
+            dtmax=0, dtmin=0, shrink=False):
         """
         Script to run to finalize gates. Currently adds waiting gates
         as required and sorts gates.
@@ -370,6 +371,12 @@ def finalize(self, topo_order=False, dtmax=0, dtmin=0, shrink=False):
         --------
         topo_order : bool
             whether to toposort gates or simply order them by time.
+        tmin : float or dict of floats
+            earliest time to add decay on qubits. If set, overrides
+            shrink.
+        tmax : float of dict of floats
+            latest time to add decay on qubits. If set, overrides
+            shrink.
         dtmax : float or dict of floats
             time to pad qubits by (i.e. dead time after the gates 
             in the circuit are executed). If float, applies same
@@ -384,6 +391,7 @@ def finalize(self, topo_order=False, dtmax=0, dtmin=0, shrink=False):
 
         if self.setup.system_params['uses_waiting_gates'] is True:
             self.add_waiting_gates(
+                tmin=tmin, tmax=tmax,
                 dtmin=dtmin, dtmax=dtmax, shrink=shrink)
 
         if topo_order is True:
@@ -392,7 +400,8 @@ def finalize(self, topo_order=False, dtmax=0, dtmin=0, shrink=False):
             self.circuit.gates = sorted(self.circuit.gates,
                                         key=lambda x: x.time)
 
-    def add_waiting_gates(self, dtmin=0, dtmax=0, shrink=False):
+    def add_waiting_gates(self, tmin=None, tmax=None,
+            dtmin=0, dtmax=0, shrink=False):
         """
         Function to add waiting gates to system
 
@@ -409,13 +418,17 @@ def add_waiting_gates(self, dtmin=0, dtmax=0, shrink=False):
         shrink : bool
             whether to shrink resting gates around qubits. When
         """
-        if shrink:
-            tmin = self.tmins
-            tmax = self.times
-        else:
-            circuit_time = max(self.times.values())
-            tmax = {key: circuit_time for key in self.times.keys()}
-            tmin = {key: 0 for key in self.times.keys()}
+        if tmin is None:
+            if shrink:
+                tmin = self.tmins
+            else:
+                tmin = {key: 0 for key in self.times.keys()}
+        if tmax is None:
+            if shrink:
+                tmax = self.times
+            else:
+                circuit_time = max(self.times.values())
+                tmax = {key: circuit_time for key in self.times.keys()}
 
         if type(dtmax) == dict:
             for key,val in dtmax.items():

From 8e6d8f66e64665fc1313b08bc4e5d431189c96aa Mon Sep 17 00:00:00 2001
From: Thomas OBrien <obrien@lorentz.leidenuniv.nl>
Date: Tue, 6 Nov 2018 14:15:11 +0100
Subject: [PATCH 3/5] Adjusted circuit_builder to use simple order

---
 qsoverlay/circuit_builder.py | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/qsoverlay/circuit_builder.py b/qsoverlay/circuit_builder.py
index 63344f8..ed3578d 100644
--- a/qsoverlay/circuit_builder.py
+++ b/qsoverlay/circuit_builder.py
@@ -361,16 +361,17 @@ def update(self, **kwargs):
         for rule in self.update_rules:
             update_function_dic[rule](self, **kwargs)
 
-    def finalize(self, topo_order=False, tmin=None, tmax=None,
-            dtmax=0, dtmin=0, shrink=False):
+    def finalize(self, toposort=False, tmin=None, tmax=None,
+                 dtmax=0, dtmin=0, shrink=False):
         """
         Script to run to finalize gates. Currently adds waiting gates
         as required and sorts gates.
 
         Args:
         --------
-        topo_order : bool
+        toposort : bool or "simple"
             whether to toposort gates or simply order them by time.
+            Setting toposort="simple" uses the simple toposort algorithm.
         tmin : float or dict of floats
             earliest time to add decay on qubits. If set, overrides
             shrink.
@@ -394,11 +395,7 @@ def finalize(self, topo_order=False, tmin=None, tmax=None,
                 tmin=tmin, tmax=tmax,
                 dtmin=dtmin, dtmax=dtmax, shrink=shrink)
 
-        if topo_order is True:
-            self.circuit.order()
-        else:
-            self.circuit.gates = sorted(self.circuit.gates,
-                                        key=lambda x: x.time)
+        self.circuit.order(toposort)
 
     def add_waiting_gates(self, tmin=None, tmax=None,
             dtmin=0, dtmax=0, shrink=False):

From 258079ef0a24c6040e58f3fab7b7ceae5ea6c3cd Mon Sep 17 00:00:00 2001
From: Thomas OBrien <obrien@lorentz.leidenuniv.nl>
Date: Thu, 31 Jan 2019 15:12:37 +0100
Subject: [PATCH 4/5] Added system_params to asymmetric setup

---
 qsoverlay/DiCarlo_setup.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/qsoverlay/DiCarlo_setup.py b/qsoverlay/DiCarlo_setup.py
index 7dff27e..e81f4d7 100644
--- a/qsoverlay/DiCarlo_setup.py
+++ b/qsoverlay/DiCarlo_setup.py
@@ -191,7 +191,12 @@ def asymmetric_setup(qubit_parameters=None,
         qubit_dic=asym_setup['qubit_dic'],
         gate_dic=asym_setup['gate_dic'],
         connectivity_dic=connectivity_dic)
-    return Setup(**asym_setup)
+
+    system_params = {
+        'uses_waiting_gates': True
+    }
+
+    return Setup(**asym_setup, system_params=system_params)
 
 
 def get_gate_dic():

From 6dc3bbf65101b621a387fbecb096b256ade33d2a Mon Sep 17 00:00:00 2001
From: Thomas OBrien <obrien@novamaris.lorentz.leidenuniv.nl>
Date: Thu, 27 Jun 2019 16:02:23 +0200
Subject: [PATCH 5/5] Two minor fixes

---
 qsoverlay/circuit_builder.py  | 9 +++++----
 qsoverlay/experiment_setup.py | 5 ++++-
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/qsoverlay/circuit_builder.py b/qsoverlay/circuit_builder.py
index ed3578d..83d761f 100644
--- a/qsoverlay/circuit_builder.py
+++ b/qsoverlay/circuit_builder.py
@@ -390,10 +390,11 @@ def finalize(self, toposort=False, tmin=None, tmax=None,
             whether to shrink resting gates around qubits. When
         """
 
-        if self.setup.system_params['uses_waiting_gates'] is True:
-            self.add_waiting_gates(
-                tmin=tmin, tmax=tmax,
-                dtmin=dtmin, dtmax=dtmax, shrink=shrink)
+        if ('uses_waiting_gates' in self.setup.system_params and 
+            self.setup.system_params['uses_waiting_gates'] is True):
+                self.add_waiting_gates(
+                    tmin=tmin, tmax=tmax,
+                    dtmin=dtmin, dtmax=dtmax, shrink=shrink)
 
         self.circuit.order(toposort)
 
diff --git a/qsoverlay/experiment_setup.py b/qsoverlay/experiment_setup.py
index 27e07a4..08892d9 100644
--- a/qsoverlay/experiment_setup.py
+++ b/qsoverlay/experiment_setup.py
@@ -33,7 +33,10 @@ def load(self, filename, seed=None, state=None):
 
         self.update_rules = setup_load_format['update_rules']
         self.qubit_dic = setup_load_format['qubit_dic']
-        self.system_params = setup_load_format['system_params']
+        try:
+            self.system_params = setup_load_format['system_params']
+        except:
+            self.system_params = {}
 
         # Currently assumes each qubit uses the same
         # uniform_noisy_sampler - this needs fixing