diff --git a/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_1_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_1_FBM_d_1.008.xml
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_1_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_1_SHOVE_d_1.25.xml
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_2_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_2_FBM_d_1.008.xml
new file mode 100644
index 000000000..7f0197ed7
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_2_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_2_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..bb987c200
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_3_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_3_FBM_d_1.008.xml
new file mode 100644
index 000000000..c05e168c0
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@@ -0,0 +1,214 @@
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_3_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_3_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..59f012ac7
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@@ -0,0 +1,215 @@
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_1_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_1_FBM_d_1.008.xml
new file mode 100644
index 000000000..ec82bcbf8
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+++ b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_1_FBM_d_1.008.xml
@@ -0,0 +1,214 @@
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_1_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_1_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..e5887ff11
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_2_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_2_FBM_d_1.008.xml
new file mode 100644
index 000000000..7832ac73a
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_2_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_2_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..2159f2931
--- /dev/null
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_3_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_3_FBM_d_1.008.xml
new file mode 100644
index 000000000..96af0dbf5
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_3_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_3_SHOVE_d_1.25.xml
new file mode 100644
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_standard_case_1_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_1_FBM_d_1.008.xml
new file mode 100644
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_standard_case_1_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_1_SHOVE_d_1.25.xml
new file mode 100644
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_standard_case_2_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_2_FBM_d_1.008.xml
new file mode 100644
index 000000000..1297c8144
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_standard_case_2_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_2_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..2e3329519
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_standard_case_3_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_3_FBM_d_1.008.xml
new file mode 100644
index 000000000..1534ea8a6
--- /dev/null
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diff --git a/protocol/Benchmark_3_protocols/benchmark_3_standard_case_3_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_3_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..9fa77816e
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diff --git a/protocol/numerical_testing/biofilm_no_growth.xml b/protocol/numerical_testing/biofilm_no_growth.xml
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diff --git a/protocol/numerical_testing/growing_population_in_chemostat.xml b/protocol/numerical_testing/growing_population_in_chemostat.xml
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diff --git a/protocol/numerical_testing/non_growing_catalyst_agent_chemostat.xml b/protocol/numerical_testing/non_growing_catalyst_agent_chemostat.xml
new file mode 100644
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diff --git a/protocol/numerical_testing/thin_cell_layer_no_growth.xml b/protocol/numerical_testing/thin_cell_layer_no_growth.xml
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