diff --git a/scripts/bs_Core.sh b/scripts/bs_Core.sh
deleted file mode 100755
index fd156520..00000000
--- a/scripts/bs_Core.sh
+++ /dev/null
@@ -1,54 +0,0 @@
-#!/bin/bash
-#SBATCH -J MODEL_NAME
-#SBATCH -c NCORES
-#SBATCH --time=WALL_TIME
-#SBATCH --mail-type=FAIL
-#SBATCH --mail-type=END
-#SBATCH --mail-user=NoMail
-#SBATCH --mem=MEMORYGB
-
-if [ -z "$SLURM_NPROCS" ] ; then
-  if [ -z "$SLURM_NTASKS_PER_NODE" ] ; then
-    SLURM_NTASKS_PER_NODE=1
-  fi
-  SLURM_NPROCS=$(( $SLURM_JOB_NUM_NODES * $SLURM_NTASKS_PER_NODE ))
-fi
-
-#!/bin/bash
-module load graphviz
-
-setting=""
-paramPath=""
-nMC=""
-forceFlag=""
-sweepDefs=""
-sweepfile=""
-rows=""
-
-while getopts S:n:w:W:r:Fa:p:P: option
-do
-    case "${option}"
-        in
-	S) setting=${OPTARG};;
-	n) nMC=${OPTARG};;
-	w) sweepDefs+="-w ${OPTARG} ";;
-	W) sweepfile="-W ${OPTARG}";;
-	r) rows="-r ${OPTARG}";;
-	F) forceFlag="-F";;
-	a) paramPath=${OPTARG};;
-	p) savePop="--savepop";;
-	P) popPath="--poppath ${OPTARG}";;
-    esac
-done
-
-cd $PWD
-
-echo Master process running on `hostname`
-echo Directory is `pwd`
-echo PBS has allocated the following nodes:
-echo `cat $PBS_NODEFILE`
-echo Starting execution at `date`
-NCPU=`wc -l < $PBS_NODEFILE`
-echo This job has allocated $NCPU CPUs
-
-./run_titan.py -S $setting -n $nMC -p $paramPath $forceFlag $sweepDefs $sweepfile $rows $savePop $popPath
diff --git a/settings/nyc-msm/partnership.yml b/settings/nyc-msm/partnership.yml
deleted file mode 100644
index d76b0a3b..00000000
--- a/settings/nyc-msm/partnership.yml
+++ /dev/null
@@ -1,49 +0,0 @@
-partnership:
-  sex:
-    frequency:
-      Main:
-        type: distribution
-        distribution:
-          dist_type: gamma
-          vars:
-            1:
-              value: 0.439
-              value_type: float
-            2:
-              value: 15.3
-              value_type: float
-      Casual:
-        type: distribution
-        distribution:
-          dist_type: gamma
-          vars:
-            1:
-              value: 0.131
-              value_type: float
-            2:
-              value: 16.5
-              value_type: float
-    haart_scaling:
-      MSM: # calibration
-        non_adherent: 0.165
-        adherent: 0.00
-    acquisition:
-      MSM:
-        insertive: 0.0017
-        receptive: 0.0075
-        versatile: 0.0046
-
-  duration:
-    Main:
-      type: distribution
-      distribution:
-        dist_type: wald
-        vars:
-          1:
-            value: 52.88
-            value_type: float
-          2:
-            value: 5.248
-            value_type: float
-        mean: 52.88
-
diff --git a/setup.py b/setup.py
new file mode 100644
index 00000000..972740e0
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,73 @@
+import setuptools
+import subprocess
+
+# ========= FROM https://github.com/vivin/better-setuptools-git-version/blob/master/better_setuptools_git_version.py with edits =========
+def get_latest_tag():
+    return subprocess.getoutput(
+        "git describe --tags `git rev-list --tags --max-count=1`"
+    )
+
+
+def get_tag_commit_sha(tag):
+    """Return the commit that the tag is pointing to."""
+    return subprocess.getoutput("git rev-list -n 1 {tag}".format(tag=tag))
+
+
+def get_head_sha():
+    """Return the sha key of HEAD."""
+    return subprocess.getoutput("git rev-parse HEAD")
+
+
+def is_head_at_tag(tag):
+    """Return True or False depending on whether the given tag is pointing to HEAD"""
+    return get_head_sha() == get_tag_commit_sha(tag)
+
+
+def get_version():
+    """
+    Return the full git version using the given template. If there are no annotated tags, the version specified by
+    starting_version will be used. If HEAD is at the tag, the version will be the tag itself. If there are commits ahead
+    of the tag, the first 8 characters of the sha of the HEAD commit will be included.
+    In all of the above cases, if the working tree is also dirty or contains untracked files, a "+dirty" suffix will be
+    appended to the version.
+    Returns:
+        the formatted version based on tags in the git repository.
+    """
+    template = "{tag}.dev{sha}"
+    tag = get_latest_tag()
+    if is_head_at_tag(tag):
+        version = tag
+    else:
+        sha = get_head_sha()[:8]
+        version = template.format(tag=tag, sha=sha)
+
+    return version
+
+
+# add the readme as the description
+with open("README.md", "r", encoding="utf-8") as fh:
+    long_description = fh.read()
+
+# make the requirements.txt be installed (not good practice for general packaging, good for current oscar set up)
+with open("requirements.txt") as f:
+    required = f.read().splitlines()
+
+setuptools.setup(
+    name="titan",  # Replace with your own username,
+    version=get_version(),
+    # author="Example Author",
+    # author_email="author@example.com",
+    description="TITAN Agent Based Model",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/marshall-lab/TITAN",
+    packages=setuptools.find_packages(),
+    install_requires=required,
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "Operating System :: OS Independent",
+    ],
+    python_requires=">=3.6",
+    package_data={"titan": ["params/*.yml", "settings/*/*.yml"]},
+    entry_points={"console_scripts": ["run_titan=titan:script_init"]},
+)
diff --git a/subTitan.sh b/subTitan.sh
deleted file mode 100755
index e49eb126..00000000
--- a/subTitan.sh
+++ /dev/null
@@ -1,189 +0,0 @@
-#!/bin/bash
-
-#Read in source code path, then shift for optargs
-titanPath=$PWD
-paramPath="$1"
-shift
-
-setting="custom"
-date=`date +%Y-%m-%d-T%H-%M-%S`
-user=${USER}
-walltime=12:00:00
-memory=12g
-outfile="Jobname.o"
-repeats=1
-nMC=1
-model=${PWD##*/}
-basePath=$PWD
-jobname=""
-folderName=""
-sweepDefs=""
-sweepfile=""
-rows=""
-num_cores=1
-forceFlag=""
-savePop=""
-popPath=""
-
-while getopts m:j:T:S:r:n:f:w:W:R:Fc:t:p:P: option
-do
-    case "${option}"
-        in
-	m) memory=${OPTARG};;
-	j) jobname=${OPTARG};;
-	T) walltime=${OPTARG};;
-	S) setting=${OPTARG};;
-	r) repeats=${OPTARG};;
-	n) nMC=${OPTARG};;
-	f) folderName=${OPTARG};;
-	w) sweepDefs+="-w ${OPTARG} ";;
-	W) sweepfile="-W ${OPTARG}";;
-	R) rows="-r ${OPTARG}";;
-	F) forceFlag="-F";;
-	c) num_cores=${OPTARG};;
-	t) titanPath=${OPTARG};;
-	p) savePop="-p";;
-	P) popPath="-P ${OPTARG}";;
-    esac
-done
-
-if [[ $jobname == "" ]]; then
-	jobname="Analysis_$setting_$date"
-fi
-
-if [[ $folderName == "" ]]; then
-	folderName="$setting/"
-fi
-
-srcCode="${titanPath}/titan/"
-outPath="$HOME/scratch/$folderName"
-
-usage() {
-echo "
-usage: subtitan {Parameter file or directory}[-T walltime] [-m memory] [-S setting] [-j jobname] [-r repeats] [-n iterations] [-b use_base] [-f folder_name] [-w sweep_defs] [-F force] [-c num_cores ] [-t titanPath ]
-
-Starts a TITAN simulation in ~/scratch/{SourceFolder}/{jobname}
-
-options:
-  -j jobname	  name of analysis for organization (default: {SourceFolder}_date)
-  -T walltime     as hh:mm:ss, max compute time (default: $walltime)
-  -m memory       per node, as #[k|m|g] (default: $memory)
-  -S setting      name of setting for this model
-  -r repeats      number of times to repeat the analysis (default: $repeats)
-  -n iterations   number of mode iterations per job (default: $nMC)
-  -f folder_name  What the parent folder for the model run outputs should be called (default: <setting>)
-  -w sweep_defs   Optionally, definitions of sweep parameters in the format param:start:stop[:step]
-  -W sweepfile    Optionally, a csv file with sweep definitions (if used, -w flag is ignored)
-  -R rows         Optionally, which data rows of the sweep file to use in format start:stop
-  -F force	  If the number of sweep combinations exceeds 100, run anyway
-  -c num_cores	  How many cores to request and run the job on (default: $num_cores)
-  -t titanPath	  where the code is
-	-p savePop			save population, either 'all' or 'core' (default none)
-	-P popPath			load population from the provide path (by default, creates a new population)
-"
-exit 0
-}
-
-updateParams() {
-echo "
-
-    Updating params:
-	savePath	$PWD
-	sourceCode	$srcCode
-	jobname 	$jobname
-	walltime	$walltime
-	memory		$memory
-	num_cores	$num_cores
-"
-
-#Submit script params
-sed -i "s/MODEL_NAME/$jobname/g" scripts/bs_Core.sh
-sed -i "s/WALL_TIME/$walltime/g" scripts/bs_Core.sh
-sed -i "s/MEMORY/$memory/g" scripts/bs_Core.sh
-sed -i "s/NCORES/$num_cores/g" scripts/bs_Core.sh
-
-}
-
-prepSubmit() {
-    #Copy source code into parent path
-    echo -e "\n\tCopying $srcCode to $finalPath"
-    mkdir -p $finalPath
-    cp $titanPath/run_titan.py $finalPath
-    cp -rT $titanPath/titan $finalPath/titan
-    cp -rT $titanPath/scripts $finalPath/scripts
-	  cp -rT $titanPath/settings $finalPath/settings
-    #Move into new source code folder
-    echo -e "\n\tMoving to model folder directory"
-    cd $finalPath
-    echo -e "\t$PWD"
-    updateParams;
-
-    #Submit job to cluster
-    sbatch scripts/bs_Core.sh -S $setting -a $paramPath -n $nMC $forceFlag $sweepDefs $sweepfile $rows $savePop $popPath
-
-    #Move back to base directory
-    cd $basePath
-}
-
-
-# User and Date will be ignored if job ID is specified
-
-if [ ! $paramPath ]; then
-    usage;
-fi
-
-if [[ ${paramPath:0:1} != "/" ]] || [[ ${paramPath:0:1} == "~" ]]; then
-	paramPath="${pwd}/$paramPath"
-fi
-
-if [ ! -d $srcCode ]; then
-    echo -e "\n\n$srcCode is not a directory! Source code must be provided as a directory\n"
-    exit 0
-fi
-
-if [ -d $outPath$jobname ]; then
-    echo -e "\n\n!! WARNING !!\nThe folder $jobname already exists and will be OVERWRITTEN!\n"
-    read -p "Continue (y/n)?" choice
-    case "$choice" in
-      y|Y ) echo "Proceeding";;
-      n|N|* ) echo "Aborting"
-	    exit 0;;
-    esac
-fi
-
-if [ $srcCode ]; then
-
-    echo "
-        jobname     $jobname
-        outPath	    $outPath
-        paramPath   $paramPath
-        user        $user
-        date        $date
-        walltime    $walltime
-        memory      $memory
-        outfile     $outfile
-        model       $model"
-    echo -e "\n"
-
-    echo -e "\tMaking parent directory in scratch"
-    mkdir -p $outPath
-    echo -e "\t $outPath"
-
-    if [ $repeats -gt 1 ]; then
-        # mkdir -p $outPath$jobname
-        basejobname=$jobname
-        for ((i=1; i<=repeats; i++)); do
-            echo -e "\n\nWorking on repeat $i"
-            jobname=$basejobname"_"$i
-            finalPath=$outPath"/"$basejobname"/"$jobname
-            prepSubmit;
-        done
-    else
-        finalPath=$outPath"/"$jobname
-        prepSubmit;
-    fi
-
-else
-    echo -e "\nSOMETHING WENT WRONG!!! Abort"
-    exit 1;
-fi
diff --git a/tests/features/haart_test.py b/tests/features/haart_test.py
index fd535a8e..a9694dfd 100644
--- a/tests/features/haart_test.py
+++ b/tests/features/haart_test.py
@@ -18,6 +18,7 @@ def test_update_haart_t1(make_model, make_agent):
 
     # t0 agent initialized HAART
     a.hiv.dx = True
+    a.hiv.dx_time = model.time
 
     # go on haart
     model.run_random = FakeRandom(
@@ -35,7 +36,7 @@ def test_update_haart_t1(make_model, make_agent):
     assert a.haart.active is False
 
     # Try haart cap with low cap, one agent on haart and one diagnosed agent. Nothing happens
-    a.location.params.hiv.haart_cap = True
+    a.location.params.haart.use_cap = True
     a.haart.counts[a.race][a.sex_type] = 1
     a.hiv.dx_counts[a.race][a.sex_type] = 5
     a.location.params.demographics[a.race].sex_type[a.sex_type].drug_type[
@@ -48,7 +49,52 @@ def test_update_haart_t1(make_model, make_agent):
     # Increase cap. Agent goes on haart
     a.location.params.demographics[a.race].sex_type[a.sex_type].drug_type[
         a.drug_type
-    ].haart.prob = 2.0
+    ].haart.cap = 2.0
     a.haart.update_agent(model)
     assert a.haart.active
     assert a.haart.adherent is True
+
+    # falls off adherence
+    model.run_random = FakeRandom(1.0)
+    a.location.params.demographics[a.race].sex_type[a.sex_type].drug_type[
+        a.drug_type
+    ].haart.adherence.discontinue = 5.0
+    a.haart.update_agent(model)
+    assert a.haart.active
+    assert a.haart.adherent is False
+
+
+def test_update_haart_dx_time(make_model, make_agent):
+    model = make_model()
+    model.time = 1
+    a = make_agent(race="white")
+    model.run_random = FakeRandom(0.5)
+
+    a.hiv.active = True
+    a.hiv.dx = True
+    a.hiv.dx_time = model.time  # agent dx duration is 0
+    a.haart.update_agent(model)
+    assert not a.haart.active
+
+    a.hiv.dx_time -= 10
+    a.haart.update_agent(model)
+    assert a.haart.active
+
+
+def test_update_haart_reinit(make_model, make_agent):
+    model = make_model()
+    model.time = 1
+    a = make_agent(race="white")
+
+    a.hiv.active = True
+    a.hiv.dx = True
+    a.hiv.dx_time = model.time - 1  # make duration 1, would pass if not reinit
+    a.haart.ever = True  # uses reinit prob
+    a.haart.update_agent(model)
+    assert not a.haart.active
+
+    a.location.params.demographics[a.race].sex_type[a.sex_type].drug_type[
+        a.drug_type
+    ].haart.reinit.prob = 1.0
+    a.haart.update_agent(model)
+    assert a.haart.active
diff --git a/tests/features/prep_test.py b/tests/features/prep_test.py
index aa1e632e..034b4bfb 100644
--- a/tests/features/prep_test.py
+++ b/tests/features/prep_test.py
@@ -199,7 +199,7 @@ def test_initiate_prep_eligible(make_model, make_agent):
     p.hiv.dx = True
     p.external_exposure.active = True
     model.time = 10
-    a.location.params.prep.target = 1.0
+    a.location.params.prep.cap = 1.0
     a.location.params.prep.target_model = ["cdc_women"]
     rel = Relationship(a, p, 10, bond_type="Sex")
     # non-forcing, adherant, inj
@@ -223,7 +223,7 @@ def test_initiate_prep_eligible_racial(make_model, make_agent):
     p.hiv.dx = True
     p.external_exposure.active = True
     model.time = 10
-    a.location.params.prep.target = 1.0
+    a.location.params.prep.cap = 1.0
     a.location.params.prep.target_model = ["Racial"]
     rel = Relationship(a, p, 10, bond_type="Sex")
     # non-forcing, adherant, inj
@@ -383,10 +383,10 @@ def test_progress_inj_prep(make_agent, params, make_model):
 
 
 @pytest.mark.unit
-def test_target_as_prob(make_agent, make_model, params):
+def test_cap_as_prob(make_agent, make_model, params):
     model = make_model(params)
     a = make_agent()
-    a.location.params.prep.target_as_prob = True
+    a.location.params.prep.cap_as_prob = True
 
     model.run_random = FakeRandom(0.2)
     a.prep.initiate(model)
diff --git a/tests/features/random_trial_test.py b/tests/features/random_trial_test.py
index 28a41e81..0bc2ffe5 100644
--- a/tests/features/random_trial_test.py
+++ b/tests/features/random_trial_test.py
@@ -10,7 +10,7 @@
 def test_initialize_random_trial_prep_all(make_model, params):
     params.features.prep = True
     params.vaccine.on_init = False
-    params.prep.target = 0
+    params.prep.cap = 0
     params.random_trial.choice = "all"
     model = make_model(params)
     model.run_random = FakeRandom(-0.1)
@@ -27,7 +27,7 @@ def test_initialize_random_trial_prep_all(make_model, params):
 def test_initialize_random_trial_prep_eigenvector(make_model, params):
     params.features.prep = True
     params.vaccine.on_init = False
-    params.prep.target = 0
+    params.prep.cap = 0
     params.hiv.start_time = 5
     params.random_trial.choice = "eigenvector"
     model = make_model(params)
@@ -53,7 +53,7 @@ def test_initialize_random_trial_prep_eigenvector(make_model, params):
 def test_initialize_random_trial_prep_random(make_model, params):
     params.features.prep = True
     params.vaccine.on_init = False
-    params.prep.target = 0
+    params.prep.cap = 0
     params.hiv.start_time = 5
     params.random_trial.choice = "random"
     model = make_model(params)
diff --git a/tests/integration_test.py b/tests/integration_test.py
index 5f9431a4..9de11b30 100644
--- a/tests/integration_test.py
+++ b/tests/integration_test.py
@@ -30,7 +30,9 @@ def _make_model_integration():
 
 @pytest.mark.integration_deterministic
 def test_model_runs():
-    f = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "run_titan.py")
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
     param_file = os.path.join(
         os.path.dirname(os.path.abspath(__file__)), "params", "basic.yml"
     )
@@ -39,11 +41,26 @@ def test_model_runs():
     assert True
 
 
+@pytest.mark.integration_deterministic
+def test_model_runs_sweep():
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
+    param_file = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "params", "basic.yml"
+    )
+
+    subprocess.check_call([f, f"-p {param_file}", "-w model.seed.run:1:3"])
+    assert True
+
+
 @pytest.mark.integration_deterministic
 def test_model_reproducible(tmpdir):
     path_a = tmpdir.mkdir("result_a")
     path_b = tmpdir.mkdir("result_b")
-    f = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "run_titan.py")
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
     param_file = os.path.join(
         os.path.dirname(os.path.abspath(__file__)), "params", "basic_seeded.yml"
     )
@@ -80,7 +97,9 @@ def test_model_reproducible(tmpdir):
 @pytest.mark.integration_deterministic
 def test_model_pop_write_read(tmpdir):
     path_a = tmpdir.mkdir("a")
-    f = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "run_titan.py")
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
     param_file = os.path.join(
         os.path.dirname(os.path.abspath(__file__)), "params", "basic.yml"
     )
@@ -99,13 +118,17 @@ def test_model_pop_write_read(tmpdir):
 
 @pytest.mark.integration_deterministic
 def test_model_settings_run(tmpdir):
-    f = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "run_titan.py")
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
     param_file = os.path.join(
         os.path.dirname(os.path.abspath(__file__)), "params", "integration_base.yml"
     )
 
     for item in os.listdir(
-        os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "settings")
+        os.path.join(
+            os.path.dirname(os.path.abspath(__file__)), "..", "titan", "settings"
+        )
     ):
         if "__" not in item and item != "base":
             path = tmpdir.mkdir(item)
@@ -189,7 +212,7 @@ def test_prep_coverage(make_model_integration, tmpdir):
     model_a.run(path_a)
 
     # change the coverage upward for creating model b, use same seeds
-    model_a.params.prep.target = 0.9
+    model_a.params.prep.cap = 0.9
     model_a.params.prep.init = 0.9
     model_a.params.model.seed.run = model_a.run_seed
     model_a.params.model.seed.ppl = model_a.pop.pop_seed
@@ -197,7 +220,7 @@ def test_prep_coverage(make_model_integration, tmpdir):
     model_b = TITAN(model_a.params)
     model_b.run(path_b)
     print(
-        f"model b prep world target: {model_b.pop.geography.locations['world'].params.prep.target}"
+        f"model b prep world cap: {model_b.pop.geography.locations['world'].params.prep.cap}"
     )
 
     result_file_a = os.path.join(path_a, "basicReport.txt")
@@ -232,6 +255,7 @@ def test_prep_coverage(make_model_integration, tmpdir):
     t10_hiv_b = res_b["10"]["hiv"]
     t10_diff = t10_hiv_a - t10_hiv_b  # a should be higher
     assert res_a["10"]["prep"] < res_b["10"]["prep"]
+    assert t10_hiv_a > t0_hiv_a
     assert t10_diff > t0_diff
 
 
@@ -242,11 +266,13 @@ def test_syringe_services(params_integration, tmpdir):
     """
     params_integration.demographics.black.sex_type.MSM.drug_type.Inj.ppl = 1.0
     params_integration.demographics.black.sex_type.MSM.drug_type["None"].ppl = 0.0
+    params_integration.model.num_pop = 500
     model_a = TITAN(params_integration)
-    model_a.params.partnership.sex.frequency.Sex = ObjMap(
-        {"type": "bins", "bins": {1: {"prob": 1.0, "min": 0, "max": 1}}}
+    model_a.params.partnership.sex.frequency.Sex = (
+        ObjMap(  # turn off sex to show only injection effects
+            {"type": "bins", "bins": {1: {"prob": 1.0, "min": 0, "max": 1}}}
+        )
     )
-
     path_a = tmpdir.mkdir("a")
     path_a.mkdir("network")
     path_b = tmpdir.mkdir("b")
@@ -254,6 +280,15 @@ def test_syringe_services(params_integration, tmpdir):
 
     # run with default bins (0-9)
     model_a.run(path_a)
+    num_bonds = 0
+    num_ag = 0
+    for ag in model_a.pop.all_agents:
+        if ag.hiv.active:
+            num_ag += 1
+            for ptnr in ag.get_partners(["Inj", "SexInj"]):
+                if not ptnr.hiv.active:
+                    num_bonds += 1
+    assert num_bonds  # make sure there are serodiscordant partnerships
 
     # change the coverage upward for creating model b, use same seeds
     model_a.params.features.syringe_services = True
@@ -290,6 +325,8 @@ def test_syringe_services(params_integration, tmpdir):
     t10_hiv_a = res_a["10"]
     t10_hiv_b = res_b["10"]
     t10_diff = t10_hiv_a - t10_hiv_b  # a should be higher
+    assert t10_hiv_a > t0_hiv_a
+    assert t10_hiv_b > t0_hiv_b
     assert t10_diff > t0_diff
 
 
diff --git a/tests/model_test.py b/tests/model_test.py
index 36b4bbf7..e9ba2e52 100644
--- a/tests/model_test.py
+++ b/tests/model_test.py
@@ -141,21 +141,21 @@ def test_timeline_scaling_prep_def(make_model):
     model.params.timeline_scaling.timeline = ObjMap(
         {
             "scale": {
-                "parameter": "prep|target",
+                "parameter": "prep|cap",
                 "start_time": 1,
                 "stop_time": 3,
                 "scalar": scalar,
             }
         }
     )
-    original_prep_target = model.params.prep.target
+    original_prep_target = model.params.prep.cap
 
     # scale the param
     model.time = 1
     model.timeline_scaling()
 
     assert math.isclose(
-        original_prep_target * scalar, model.params.prep.target, abs_tol=0.001
+        original_prep_target * scalar, model.params.prep.cap, abs_tol=0.001
     )
 
     # param still scaled
@@ -163,17 +163,17 @@ def test_timeline_scaling_prep_def(make_model):
     model.timeline_scaling()
 
     assert math.isclose(
-        original_prep_target * scalar, model.params.prep.target, abs_tol=0.001
+        original_prep_target * scalar, model.params.prep.cap, abs_tol=0.001
     )
 
     # revert to original
     model.time = 3
     model.timeline_scaling()
 
-    assert math.isclose(original_prep_target, model.params.prep.target, abs_tol=0.001)
+    assert math.isclose(original_prep_target, model.params.prep.cap, abs_tol=0.001)
 
     # still original
     model.time = 4
     model.timeline_scaling()
 
-    assert math.isclose(original_prep_target, model.params.prep.target, abs_tol=0.001)
+    assert math.isclose(original_prep_target, model.params.prep.cap, abs_tol=0.001)
diff --git a/tests/params/basic.yml b/tests/params/basic.yml
index dfda011e..de5970c0 100644
--- a/tests/params/basic.yml
+++ b/tests/params/basic.yml
@@ -41,7 +41,17 @@ demographics:
                 init: 0.1
             haart:
               init: 0.1
-              prob: 0.1
+              enroll: &haart_prob
+                0:
+                  prob: 0.1
+                  start: 0
+                  stop: 10
+                1:
+                  prob: 1.0
+                  start: 10
+                  stop: 100
+              reinit: &reinit_prob
+                prob: 0.0
               adherence:
                 init: 0.1
                 prob: 0.1
@@ -64,7 +74,8 @@ demographics:
                     value_type: float
             haart:
               init: 0.1
-              prob: 0.1
+              enroll: *haart_prob
+              reinit: *reinit_prob
               adherence:
                 init: 0.1
                 prob: 0.1
@@ -73,14 +84,20 @@ demographics:
         incar: &base_incar
           init: 0.02
           prob: 0.02
-        safe_sex: 0.1
+        safe_sex: &safe_sex_default
+          Sex:
+            prob: 0.1
+          Inj:
+            prob: 0.1
+          SexInj:
+            prob: 0.1
         injection: &base_injection
           unsafe_prob: 0.1
           num_acts: 10
         prep: &base_prep
           adherence: 0.1
           discontinue: 0.1
-          target: 0.3
+          cap: 0.3
           init: 0.3
         high_risk: &base_high_risk
           init: 0.1
@@ -94,12 +111,12 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep:
           adherence: 0.1
           discontinue: 0.1
-          target: 0.3
+          cap: 0.3
           init: 0.5
         high_risk: *base_high_risk
         vaccine: *base_vaccine
@@ -107,7 +124,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -116,7 +133,7 @@ demographics:
         ppl: 0.2
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -125,7 +142,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -137,7 +154,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -146,7 +163,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -155,7 +172,7 @@ demographics:
         ppl: 0.2
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -164,7 +181,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection:
           unsafe_prob: 0.
           num_acts: 10
@@ -175,7 +192,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection:
           unsafe_prob: 0.
           num_acts: 10
@@ -217,40 +234,54 @@ partnership:
         receptive: 0.0138
         versatile: 0.00745
   duration:
-    Sex:
-      type: bins
-      bins:
-        1:
-          prob: 1.0
-          min: 1
-          max: 2
-    Inj:
-      type: distribution
-      distribution:
-        dist_type: randint
-        vars:
+    Sex: 
+      white:
+        type: bins
+        bins:
           1:
-            value: 1
-            value_type: int
-          2:
-            value: 3
-            value_type: int
-        mean: 1
-    SexInj: &poisson_one
-      type: distribution
-      distribution:
-        dist_type: poisson
-        vars:
+            prob: 1.0
+            min: 1
+            max: 2
+      black:
+        type: bins
+        bins:
           1:
-            value: 1
-            value_type: float
-        mean: 1
-    Social: *poisson_one
+            prob: 1.0
+            min: 3
+            max: 4
+    Inj:
+      white: &inj_dur
+        type: distribution
+        distribution:
+          dist_type: randint
+          vars:
+            1:
+              value: 1
+              value_type: int
+            2:
+              value: 3
+              value_type: int
+          mean: 1
+      black: *inj_dur
+    SexInj:
+      white: &poisson_one
+        type: distribution
+        distribution:
+          dist_type: poisson
+          vars:
+            1:
+              value: 1
+              value_type: float
+          mean: 1
+      black: *poisson_one
+    Social:
+      white: *poisson_one
+      black: *poisson_one
 
 prep:
-  target: 0.1
+  cap: 0.1
   init: 0.7
-  target_as_prob: false
+  cap_as_prob: false
 
 knowledge:
   prob: 0.3
@@ -282,6 +313,9 @@ exposures:
   hiv: true
   knowledge: true
 
+haart:
+  use_reinit: true
+
 features:
   incar: true
   prep: true
diff --git a/tests/params/basic_seeded.yml b/tests/params/basic_seeded.yml
index b5837111..a6dc0cea 100644
--- a/tests/params/basic_seeded.yml
+++ b/tests/params/basic_seeded.yml
@@ -41,7 +41,11 @@ demographics:
                 init: 0.1
             haart:
               init: 0.1
-              prob: 0.1
+              prob:
+                0:
+                  enroll: 0.1
+                  start: 0
+                  stop: 99
               adherence:
                 init: 0.1
                 prob: 0.1
@@ -64,7 +68,11 @@ demographics:
                     value_type: float
             haart:
               init: 0.1
-              prob: 0.1
+              prob:
+                0:
+                  enroll: 0.1
+                  start: 0
+                  stop: 99
               adherence:
                 init: 0.1
                 prob: 0.1
@@ -73,14 +81,22 @@ demographics:
         incar: &base_incar
           init: 0.02
           prob: 0.02
-        safe_sex: 0.1
+        safe_sex: &safe_sex_default
+          Sex:
+            prob: 0.1
+          Inj:
+            prob: 0.1
+          SexInj:
+            prob: 0.1
+          Social:
+            prob: 0.1
         injection: &base_injection
           unsafe_prob: 0.1
           num_acts: 10
         prep: &base_prep
           adherence: 0.1
           discontinue: 0.1
-          target: 0.3
+          cap: 0.3
           init: 0.3
         high_risk: &base_high_risk
           init: 0.1
@@ -94,12 +110,12 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep:
           adherence: 0.1
           discontinue: 0.1
-          target: 0.3
+          cap: 0.3
           init: 0.5
         high_risk: *base_high_risk
         vaccine: *base_vaccine
@@ -107,7 +123,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -116,7 +132,7 @@ demographics:
         ppl: 0.2
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -125,7 +141,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -137,7 +153,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -146,7 +162,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -155,7 +171,7 @@ demographics:
         ppl: 0.2
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -164,7 +180,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection:
           unsafe_prob: 0.
           num_acts: 10
@@ -175,7 +191,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection:
           unsafe_prob: 0.
           num_acts: 10
@@ -248,9 +264,9 @@ partnership:
     Social: *poisson_one
 
 prep:
-  target: 0.1
+  cap: 0.1
   init: 0.7
-  target_as_prob: false
+  cap_as_prob: false
 
 knowledge:
   prob: 0.3
diff --git a/tests/params/basic_seeded_error.yml b/tests/params/basic_seeded_error.yml
index 83cc3f7e..373ec902 100644
--- a/tests/params/basic_seeded_error.yml
+++ b/tests/params/basic_seeded_error.yml
@@ -41,7 +41,11 @@ demographics:
                 init: 0.1
             haart:
               init: 0.1
-              prob: 0.1
+              prob:
+                0:
+                  enroll: 0.1
+                  start: 0
+                  stop: 99
               adherence:
                 init: 0.1
                 prob: 0.1
@@ -64,7 +68,11 @@ demographics:
                     value_type: float
             haart:
               init: 0.1
-              prob: 0.1
+              prob:
+                0:
+                  enroll: 0.1
+                  start: 0
+                  stop: 99
               adherence:
                 init: 0.1
                 prob: 0.1
@@ -73,14 +81,22 @@ demographics:
         incar: &base_incar
           init: 0.02
           prob: 0.02
-        safe_sex: 0.1
+        safe_sex: &safe_sex_default
+          Sex:
+            prob: 0.1
+          Inj:
+            prob: 0.1
+          SexInj:
+            prob: 0.1
+          Social:
+            prob: 0.1
         injection: &base_injection
           unsafe_prob: 0.1
           num_acts: 10
         prep: &base_prep
           adherence: 0.1
           discontinue: 0.1
-          target: 0.3
+          cap: 0.3
           init: 0.3
         high_risk: &base_high_risk
           init: 0.1
@@ -94,12 +110,12 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep:
           adherence: 0.1
           discontinue: 0.1
-          target: 0.3
+          cap: 0.3
           init: 0.5
         high_risk: *base_high_risk
         vaccine: *base_vaccine
@@ -107,7 +123,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -116,7 +132,7 @@ demographics:
         ppl: 0.2
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -125,7 +141,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -137,7 +153,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -146,7 +162,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -155,7 +171,7 @@ demographics:
         ppl: 0.2
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -164,7 +180,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection:
           unsafe_prob: 0.
           num_acts: 10
@@ -175,7 +191,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection:
           unsafe_prob: 0.
           num_acts: 10
@@ -248,9 +264,9 @@ partnership:
     Social: *poisson_one
 
 prep:
-  target: 0.1
+  cap: 0.1
   init: 0.7
-  target_as_prob: false
+  cap_as_prob: false
 
 knowledge:
   prob: 0.3
diff --git a/tests/params/simple_integration.yml b/tests/params/simple_integration.yml
index 81a550a8..508af68f 100644
--- a/tests/params/simple_integration.yml
+++ b/tests/params/simple_integration.yml
@@ -20,13 +20,20 @@ demographics:
         ppl: 1.0
         incar:
           prob: 0.5 # default is off, so this only hits when turned on in integration test
-        safe_sex: 0.1
+        safe_sex:
+          Sex:
+            prob: 1.0
+          SexInj:
+            prob: 1.0
+          Inj:
+            prob: 1.0
         injection:
-          unsafe_prob: 0.1
+          unsafe_prob: 0.3
+          num_acts: 10
         prep:
           adherence: 0.9
           discontinue: 0.1
-          target: 0.3
+          cap: 0.3
           init: 0.3
         high_risk:
           init: 0.1
@@ -48,7 +55,11 @@ demographics:
                 init: 0.1
             haart:
               init: 0.1
-              prob: 0.1
+              prob:
+                1:
+                  enroll: 0.1
+                  start: 0
+                  stop: 999
               adherence:
                 init: 0.1
                 prob: 0.1
@@ -89,7 +100,11 @@ demographics:
                 init: 0.1
             haart:
               init: 0.1
-              prob: 0.1
+              prob:
+                1:
+                  enroll: 0.1
+                  start: 0
+                  stop: 999
               adherence:
                 init: 0.1
                 prob: 0.1
@@ -151,7 +166,7 @@ partnership:
 syringe_services:
   timeline:
     ssp_open:
-      start_time: 2
+      start_time: 0
       stop_time: 12
       num_slots_start: 500
       num_slots_stop: 500
@@ -161,7 +176,7 @@ partner_tracing:
   prob: 1
 
 prep:
-  target: 0.1
+  cap: 0.1
   init: 0.1
   start_time: -6
 
diff --git a/tests/partnering_test.py b/tests/partnering_test.py
index 74951f6c..8bee6c36 100644
--- a/tests/partnering_test.py
+++ b/tests/partnering_test.py
@@ -11,9 +11,11 @@
 
 def test_partnership_duration(params):
     # test duration with randint
-    assert get_partnership_duration(params, FakeRandom(1.0), "Inj") == 1
+    assert get_partnership_duration(params, FakeRandom(1.0), "Inj", "white") == 1
     # test duration with bins
-    assert get_partnership_duration(params, FakeRandom(0.1), "Sex") == 1
+    assert get_partnership_duration(params, FakeRandom(0.1), "Sex", "white") == 1
+    # test duration with second race
+    assert get_partnership_duration(params, FakeRandom(0.1), "Sex", "black") == 3
 
 
 @pytest.mark.unit
diff --git a/tests/population_io_test.py b/tests/population_io_test.py
index 3c60b4b4..38a20894 100644
--- a/tests/population_io_test.py
+++ b/tests/population_io_test.py
@@ -96,7 +96,7 @@ def test_read_pop(tmpdir, make_population, params):
 
 @pytest.mark.unit
 def test_write_read_pop_compressed(tmpdir, make_population, params):
-    params.prep.target = 0.5
+    params.prep.cap = 0.5
     pop = make_population(n=10)
     prep_counts = deepcopy(Prep.counts)
 
diff --git a/tests/population_test.py b/tests/population_test.py
index a939a675..c7e1cdaa 100644
--- a/tests/population_test.py
+++ b/tests/population_test.py
@@ -248,7 +248,7 @@ def test_update_agent_partners_MSM_match(make_population, params):
 def test_update_agent_partners_NDU_PWID_match(make_population, params):
     pop = make_population(n=0)
     a = pop.create_agent(pop.geography.locations["world"], "white", 0, "MSM")
-    p = pop.create_agent(pop.geography.locations["world"], "white", 0, "MSM")
+    p = pop.create_agent(pop.geography.locations["world"], "black", 0, "MSM")
     # ensure random sex partner no assorting
     pop.pop_random = FakeRandom(1.1)
     a.drug_type = "None"
@@ -265,6 +265,17 @@ def test_update_agent_partners_NDU_PWID_match(make_population, params):
     assert p in pop.graph.nodes()
     assert a.partners
     assert len(pop.graph.edges()) == 1
+    for (
+        rel
+    ) in (
+        a.relationships
+    ):  # check that duration uses "randomly selected" (first) partner
+        assert rel.duration == partnering.get_partnership_duration(
+            a.location.params, pop.np_random, "Sex", a.race
+        )
+        assert rel.duration != partnering.get_partnership_duration(
+            a.location.params, pop.np_random, "Sex", p.race
+        )
 
 
 @pytest.mark.unit
diff --git a/tests/run_titan_test.py b/tests/run_titan_test.py
new file mode 100644
index 00000000..2445e589
--- /dev/null
+++ b/tests/run_titan_test.py
@@ -0,0 +1,65 @@
+import pytest
+
+from titan.run_titan import *
+
+
+@pytest.mark.unit
+def test_sweep_range():
+    assert sweep_range("param:1:2") == {
+        "start": 1,
+        "stop": 2,
+        "step": 1,
+        "param": "param",
+    }
+    assert sweep_range("param:1.5:2:0.5") == {
+        "start": 1.5,
+        "stop": 2.0,
+        "step": 0.5,
+        "param": "param",
+    }
+
+    with pytest.raises(ValueError):
+        sweep_range("param:a:b:c")
+
+
+@pytest.mark.unit
+def test_drange():
+    start = 1
+    step = 0.1
+    stop = 2
+    i = 0
+    for val in drange(start, stop, step):
+        i += 1
+        assert val >= start and val < stop
+
+    assert i == 10
+
+
+@pytest.mark.unit
+def test_setup_sweeps():
+    sweeps = [
+        {"start": 1.5, "stop": 2.3, "step": 0.5, "param": "param1"},
+        {"start": 1, "stop": 4, "step": 1, "param": "param2"},
+    ]
+
+    defs = setup_sweeps(sweeps)
+
+    assert len(defs) == 6
+
+
+@pytest.mark.unit
+def test_setup_seepfile():
+    sweepfile = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "params", "sweepfile.csv"
+    )
+    rows = None
+    defs = setup_sweeps_file(sweepfile, rows)
+
+    assert len(defs) == 7
+    assert defs[0] == {"model.seed.run": 0, "model.seed.ppl": 0}
+
+    rows = "2:3"
+    defs = setup_sweeps_file(sweepfile, rows)
+
+    assert len(defs) == 2
+    assert defs[0] == {"model.seed.run": 1, "model.seed.ppl": 1}
diff --git a/titan/__init__.py b/titan/__init__.py
index 00adb5e6..6e01ee0c 100644
--- a/titan/__init__.py
+++ b/titan/__init__.py
@@ -1 +1,2 @@
 # makes src a package
+from .run_titan import script_init
diff --git a/titan/exposures/hiv.py b/titan/exposures/hiv.py
index 82004c77..19097c93 100644
--- a/titan/exposures/hiv.py
+++ b/titan/exposures/hiv.py
@@ -325,12 +325,7 @@ def progress_to_aids(self, model: "model.TITAN"):
              model: the running model
         """
         aids_params = self.agent.location.params.hiv.aids
-        p = 1.0
-        if self.agent.haart.active:  # type: ignore[attr-defined]
-            if self.agent.haart.adherent:  # type: ignore[attr-defined]
-                p = aids_params.haart_scale.adherent
-            else:
-                p = aids_params.haart_scale.non_adherent
+        p = self.agent.haart.aids_scale()  # type: ignore[attr-defined]
 
         if model.run_random.random() < p * aids_params.prob:
             self.aids = True
diff --git a/titan/features/haart.py b/titan/features/haart.py
index 5175b24e..a1a7acc7 100644
--- a/titan/features/haart.py
+++ b/titan/features/haart.py
@@ -26,6 +26,7 @@ def __init__(self, agent: "agent.Agent"):
         super().__init__(agent)
 
         self.active = False
+        self.ever = False
         self.adherent = False
 
     @classmethod
@@ -62,6 +63,7 @@ def init_agent(self, pop: "population.Population", time: int):
             and pop.pop_random.random() < agent_params.haart.init
         ):
             self.active = True
+            self.ever = True
             self.add_agent(self.agent)
 
             haart_adh = agent_params.haart.adherence.init
@@ -91,7 +93,7 @@ def update_agent(self, model: "model.TITAN"):
             )
             # Go on HAART
             if not self.active:
-                if self.agent.location.params.hiv.haart_cap:
+                if self.agent.location.params.haart.use_cap:
                     # if HAART is based on cap instead of prob, determine number of
                     # HAART agents based on % of diagnosed agents
                     num_dx_agents = self.agent.hiv.dx_counts[self.agent.race][  # type: ignore[attr-defined]
@@ -99,18 +101,46 @@ def update_agent(self, model: "model.TITAN"):
                     ]
                     num_haart_agents = self.counts[self.agent.race][self.agent.sex_type]
 
-                    if num_haart_agents < (haart_params.prob * num_dx_agents):
+                    # take value from dictionary for cap
+                    if num_haart_agents < (haart_params.cap * num_dx_agents):
                         self.initiate(model)
                 else:
-                    if model.run_random.random() < (
-                        haart_params.prob * model.calibration.haart.coverage
-                    ):
-                        self.initiate(model)
-            # Go off HAART
-            elif self.active and model.run_random.random() < haart_params.discontinue:
-                self.active = False
-                self.adherent = False
-                self.remove_agent(self.agent)
+                    if self.ever and self.agent.location.params.haart.use_reinit:
+                        if model.run_random.random() < haart_params.reinit.prob:
+                            self.initiate(model)
+                    else:
+                        enroll_prob = 0
+                        # Find enroll probability based on time since diagnosis
+                        haart_duration = model.time - self.agent.hiv.dx_time  # type: ignore[attr-defined]
+                        for i in haart_params.enroll.values():
+                            if i.start <= haart_duration < i.stop:
+                                enroll_prob = i.prob
+                                break
+
+                        if model.run_random.random() < (
+                            enroll_prob * model.calibration.haart.coverage
+                        ):
+                            self.initiate(model)
+
+            # Update agents on HAART
+            else:
+                # Go off HAART
+                if model.run_random.random() < haart_params.discontinue:
+                    self.active = False
+                    self.adherent = False
+                    self.remove_agent(self.agent)
+                # Become non-adherent
+                elif (
+                    self.adherent
+                    and model.run_random.random() < haart_params.adherence.discontinue
+                ):
+                    self.adherent = False
+                # Become adherent
+                elif (
+                    not self.adherent
+                    and model.run_random.random() < haart_params.adherence.become
+                ):
+                    self.adherent = True
 
     @classmethod
     def add_agent(cls, agent: "agent.Agent"):
@@ -168,6 +198,14 @@ def get_transmission_risk_multiplier(self, time: int, interaction_type: str):
 
         return prob
 
+    def aids_scale(self):
+        prob = 1.0
+        if self.active:
+            adherence = "adherent" if self.adherent else "non_adherent"
+            prob = self.agent.location.params.haart.aids_scale[adherence]
+
+        return prob
+
     # =========== HELPER METHODS ============
 
     def initiate(self, model: "model.TITAN"):
@@ -187,4 +225,5 @@ def initiate(self, model: "model.TITAN"):
 
         # Add agent to HAART class set, update agent params
         self.active = True
+        self.ever = True
         self.add_agent(self.agent)
diff --git a/titan/features/prep.py b/titan/features/prep.py
index 1e30e48e..6ff569c7 100644
--- a/titan/features/prep.py
+++ b/titan/features/prep.py
@@ -168,17 +168,17 @@ def initiate(self, model: "model.TITAN", force: bool = False):
 
         if force:
             self.enroll(model.run_random, model.time)
-        elif params.prep.target_as_prob:
+        elif params.prep.cap_as_prob:
             if "Racial" in params.prep.target_model:
                 if (
                     model.run_random.random()
                     <= params.demographics[self.agent.race]
                     .sex_type[self.agent.sex_type]
-                    .prep.target
+                    .prep.cap
                 ):
                     self.enroll(model.run_random, model.time)
             else:
-                if model.run_random.random() <= params.prep.target:
+                if model.run_random.random() <= params.prep.cap:
                     self.enroll(model.run_random, model.time)
         else:
             if "Racial" in params.prep.target_model:
@@ -191,12 +191,12 @@ def initiate(self, model: "model.TITAN", force: bool = False):
                 num_hiv_agents = len(all_hiv_agents & all_race)
                 target_prep = (len(all_race) - num_hiv_agents) * params.demographics[
                     self.agent.race
-                ].sex_type[self.agent.sex_type].prep.target
+                ].sex_type[self.agent.sex_type].prep.cap
             else:
                 num_prep_agents = sum(self.counts.values())
                 target_prep = int(
                     (model.pop.all_agents.num_members() - len(exposures.HIV.agents))
-                    * params.prep.target
+                    * params.prep.cap
                 )
 
             if num_prep_agents < target_prep:
diff --git a/titan/features/random_trial.py b/titan/features/random_trial.py
index 8ea8985a..72f420b6 100644
--- a/titan/features/random_trial.py
+++ b/titan/features/random_trial.py
@@ -152,7 +152,7 @@ def suitable_prep(agent, model) -> bool:
     if (
         not agent.hiv.active
         and not agent.prep.active
-        and model.run_random.random() < agent.location.params.prep.target
+        and model.run_random.random() < agent.location.params.prep.cap
         and not agent.vaccine.active
     ):
         return True
diff --git a/titan/interactions/sex.py b/titan/interactions/sex.py
index 298cec46..fe005c47 100644
--- a/titan/interactions/sex.py
+++ b/titan/interactions/sex.py
@@ -27,7 +27,8 @@ def get_num_acts(cls, model: "model.TITAN", rel: "agent.Relationship") -> int:
         p_safe_sex = (
             rel.agent1.location.params.demographics[rel.agent1.race]
             .sex_type[rel.agent1.sex_type]
-            .safe_sex
+            .safe_sex[rel.bond_type]
+            .prob
         )
 
         # increase condom usage if diagnosed
diff --git a/titan/output.py b/titan/output.py
index c86e9855..4d391e65 100644
--- a/titan/output.py
+++ b/titan/output.py
@@ -6,6 +6,7 @@
 import os
 
 import networkx as nx  # type: ignore
+from numpy import mean  # type: ignore
 
 from .parse_params import ObjMap
 from . import utils
@@ -284,8 +285,8 @@ def print_components(
     if f.tell() == 0:
         f.write(
             "run_id\trunseed\tpopseed\tt\tcompID\ttotalN\tNhiv\tNprep\tNtrtHIV"
-            "\tComp_Status\tPCA\tOral\tInjectable\tAware\tnidu\tcentrality\tDensity"
-            "\tEffectiveSize" + header + "\n"
+            "\tComp_Status\tPCA\tOral\tInjectable\tAware\tnidu\tcentrality\tdensity"
+            "\tEffectiveSize" + header + "\tdeg_cent\n"
         )
 
     comp_id = 0
@@ -341,6 +342,7 @@ def print_components(
             else:
                 component_status = "treatment_no_eligible"
 
+        deg_cent = mean(list(nx.degree_centrality(comp).values()))
         race_str = ""
         for race in race_list:
             race_str += "\t" + str(race_count[race])
@@ -350,7 +352,7 @@ def print_components(
             f"{nhiv}\t"
             f"{nprep}\t{ntrthiv}\t{component_status}\t{pca}\t{oral}\t{injectable_prep}"
             f"\t{aware}\t{nidu}\t{comp_centrality:.4f}\t{comp_density:.4f}"
-            f"\t{average_size:.4f}{race_str}\n"
+            f"\t{average_size:.4f}{race_str}\t{deg_cent}\n"
         )
 
         comp_id += 1
diff --git a/titan/params/demographics.yml b/titan/params/demographics.yml
index ba680e82..30300723 100644
--- a/titan/params/demographics.yml
+++ b/titan/params/demographics.yml
@@ -98,7 +98,7 @@ demographics:
             max: 1.0
           duration:
             prob:
-              type: bins
+              type: bin
               description: Binned probabilities of incarceration duration during model run
               fields:
                 prob:
@@ -137,7 +137,7 @@ demographics:
                   min: 130
                   max: 260
             init:
-              type: bins
+              type: bin
               description: Binned probabilities of incarceration duration when initializing population
               fields:
                 prob:
@@ -189,11 +189,16 @@ demographics:
             min: 0.0
             max: 1.0
         safe_sex:
-          default: 0.0
-          description: "Probability of safe sex (condom use) per sex act"
-          type: float
-          min: 0.0
-          max: 1.0
+          type: sub-dict
+          description: "Parameters controlling condom use/safe sex per sex act given bond type"
+          keys:
+            - bond_types
+          default:
+            prob:
+              default: 0.0
+              type: float
+              min: 0.0
+              max: 1.0
         prep:
           discontinue:
             default: 0.0
@@ -207,9 +212,9 @@ demographics:
             type: float
             min: 0.0
             max: 1.0
-          target:
+          cap:
             default: 0.0
-            description: "Target percentage of PrEP coverage for this population class, or probability of going on PrEP if target_as_prob is true"
+            description: "Ceiling/target percentage of PrEP coverage for this population class, or probability of going on PrEP if cap_as_prob is true"
             type: float
             min: 0.0
             max: 1.0
@@ -297,12 +302,36 @@ demographics:
                 type: float
                 min: 0.0
                 max: 1.0
-              prob:
-                default: 0.0
-                description: "Probability that an agent in this class with HIV becomes enrolled in HAART at a given time step"
+              cap:
                 type: float
+                default: 0.0
+                description: "Percent of diagnosed agents on haart if haart cap is used"
                 min: 0.0
                 max: 1.0
+              enroll:
+                type: definition
+                description: "Probability that an agent in this class with HIV becomes enrolled in HAART given the agent's time since diagnosis (unused if use_cap is true)"
+                fields:
+                  prob:
+                    type: float
+                    min: 0.0
+                    max: 1.0
+                  start:
+                    type: int
+                    min: 0
+                  stop:
+                    type: int
+                    min: 1
+                default:
+                  enroll_0:
+                    start: 0
+                    stop: 999
+                    prob: 0.0
+              reinit:
+                prob:
+                  type: float
+                  description: "Probability of reinitiating haart"
+                  default: 0.0
               adherence:
                 init:
                   default: 0.0
@@ -316,6 +345,18 @@ demographics:
                   type: float
                   min: 0.0
                   max: 1.0
+                discontinue:
+                  default: 0.0
+                  description: "Probability that an adherent agent will become nonadherent at a given timestep"
+                  type: float
+                  min: 0.0
+                  max: 1.0
+                become:
+                  default: 0.0
+                  description: "Probability that a non-adherent agent will become adherent at a given timestep"
+                  type: float
+                  min: 0.0
+                  max: 1.0
               discontinue:
                 default: 0.0
                 description: "Probability that an agent on HAART discontinues HAART in a given time step"
diff --git a/titan/params/haart.yml b/titan/params/haart.yml
new file mode 100644
index 00000000..4aec7ba3
--- /dev/null
+++ b/titan/params/haart.yml
@@ -0,0 +1,22 @@
+haart:
+  use_cap:
+    default: false
+    description: Whether "cap" defined in demographics.race.sex_type.haart.cap is used. Otherwise, haart probability is based on time since diagnosis (demographics.race.sex_type.haart.enroll).
+    type: boolean
+  use_reinit:
+    type: boolean
+    default: false
+    description: Whether a separate probability should be used for haart initiation among agents who have previously discontinued haart
+  aids_scale:
+    non_adherent:
+      description: Scalar for aids progression for agents on haart but non-adherent
+      default: 0.00368
+      type: float
+      min: 0.
+      max: 1.
+    adherent:
+      description: Scalar for aids progression for agents adherent to haart
+      default: 0.0008
+      type: float
+      min: 0.
+      max: 1.
diff --git a/titan/params/hiv.yml b/titan/params/hiv.yml
index bb6f1a49..108ef18b 100644
--- a/titan/params/hiv.yml
+++ b/titan/params/hiv.yml
@@ -31,28 +31,11 @@ hiv:
       type: float
       min: 0
       max: 1
-    haart_scale:
-      non_adherent:
-        description: Scalar for aids progression for agents on haart but non-adherent
-        default: 0.00368
-        type: float
-        min: 0.
-        max: 1.
-      adherent:
-        description: Scalar for aids progression for agents adherent to haart
-        default: 0.0008
-        type: float
-        min: 0.
-        max: 1.
   max_init_time:
     default: 42
     description: On creation, agents are randomly assigned an hiv.time, this is the maximum time
     type: int
     min: 2
-  haart_cap:
-    default: false
-    description: Whether "prob" defined in demographics.race.sex_type.haart is a percent of diagnosed, HIV+ agents instead of a per-time-step probability for HAART coverage
-    type: boolean
   start_time:
     default: 0
     description: "What timestep to start agent interactions related to hiv transmission"
diff --git a/titan/params/location.yml b/titan/params/location.yml
index cfb920e1..036675c2 100644
--- a/titan/params/location.yml
+++ b/titan/params/location.yml
@@ -6,7 +6,7 @@ location:
       - locations
     default:
       type: definition
-      description: "Definition of applying a scalar to a parameter.  The parameter should be the definition name with pipes instead of dots (e.g. `prep.target` would be `prep|target`). Some parameter categories can't be scaled, these include: model, classes, features, calibration, outputs, agent_zero, syringe_services, location.  Additionally, some fields within otherwise scalable categories cannot be changed by location if their use is not tied to a specific agent (e.g. prep.pca.choice, prep.random_trial). When a parameter is related to the interaction of an agent and a partner, the params of the location where the agent lives is typically used unless the parameter use clearly relates to the partner."
+      description: "Definition of applying a scalar to a parameter.  The parameter should be the definition name with pipes instead of dots (e.g. `prep.cap` would be `prep|cap`). Some parameter categories can't be scaled, these include: model, classes, features, calibration, outputs, agent_zero, syringe_services, location.  Additionally, some fields within otherwise scalable categories cannot be changed by location if their use is not tied to a specific agent (e.g. prep.pca.choice, prep.random_trial). When a parameter is related to the interaction of an agent and a partner, the params of the location where the agent lives is typically used unless the parameter use clearly relates to the partner."
       fields:
         field:
           type: enum
diff --git a/titan/params/partnership.yml b/titan/params/partnership.yml
index b229ca35..53b8d722 100644
--- a/titan/params/partnership.yml
+++ b/titan/params/partnership.yml
@@ -179,7 +179,8 @@ partnership:
     type: sub-dict
     keys:
       - bond_types
-    description: "Duration of relationships given bond type"
+      - races
+    description: "Duration of relationships given agent race and partnership bond type"
     default:
       type:
         type: enum
diff --git a/titan/params/prep.yml b/titan/params/prep.yml
index c1fc26d6..609a5f0d 100644
--- a/titan/params/prep.yml
+++ b/titan/params/prep.yml
@@ -7,9 +7,9 @@ prep:
       - Inj
     description: Type of PrEP used in model
     type: array
-  target:
+  cap:
     default: 0.0
-    description: Target coverage for PrEP coverage, or probability of initiating prep at a timestep if target_as_prob is true
+    description: Ceiling/target coverage for PrEP coverage, or probability of initiating prep at a timestep if cap_as_prob is true
     type: float
     min: 0
     max: 1
@@ -19,9 +19,9 @@ prep:
     type: float
     min: 0.
     max: 1.
-  target_as_prob:
+  cap_as_prob:
     default: false
-    description: If prep.target should be treated as a probability instead of a target
+    description: If prep.cap should be treated as a probability instead of a cap
     type: boolean
   start_time:
     default: 0
diff --git a/titan/params/syringe_services.yml b/titan/params/syringe_services.yml
index 8f258ff5..32ad2034 100644
--- a/titan/params/syringe_services.yml
+++ b/titan/params/syringe_services.yml
@@ -5,11 +5,9 @@ syringe_services:
       start_time:
         type: int
         description: "What time to start this prevalence of syringe services program"
-        min: 1
       stop_time:
         type: int
         description: "What time to stop this prevalence of syringe services program"
-        min: 1
       num_slots_start:
         type: int
         description: "Cap for number of available slots in SSP at beginning of time period"
diff --git a/titan/parse_params.py b/titan/parse_params.py
index 6a7dfc2a..9b7de6ab 100644
--- a/titan/parse_params.py
+++ b/titan/parse_params.py
@@ -86,7 +86,7 @@ def check_params(params: ObjMap):
 
 
 def create_params(
-    setting_path: Optional[str],
+    setting_name: Optional[str],
     param_path: str,
     outdir: str,
     error_on_unused: bool = False,
@@ -96,7 +96,7 @@ def create_params(
     or not to use the base setting. Parse and create a params (ObjMap) object.
 
     args:
-        setting_path: path to a settings file or directory or `None`
+        setting_name: path to a settings file or directory or `None`
         param_path: path to parameter file or directory
         outdir: path to directory where computed params will be saved
         error_on_unused: throw a hard error if there are unused parameters, otherwise warnings are only printed
@@ -116,8 +116,12 @@ def create_params(
     param_paths = []
 
     # merge setting and params
-    if setting_path is not None:
-        param_paths.append(setting_path)
+    if setting_name is not None:
+        # check if it's a known setting or pass it through as a path
+        if setting_name in os.listdir(os.path.join(parent, "settings")):
+            param_paths.append(os.path.join(parent, "settings", setting_name))
+        else:
+            param_paths.append(setting_name)
 
     param_paths.append(param_path)
 
diff --git a/titan/partnering.py b/titan/partnering.py
index df0436e1..ef130051 100644
--- a/titan/partnering.py
+++ b/titan/partnering.py
@@ -124,30 +124,34 @@ def get_mean_rel_duration(params: "parse_params.ObjMap"):
     args:
         params: The current model's parameters
     """
-    mean_rel_duration: Dict[str, int] = {}
+    mean_rel_duration: Dict[str, Dict] = {}
     for bond in params.partnership.duration:
-        if params.partnership.duration[bond].type == "bins":
-            weights = []
-            vals = []
-            dur_bins = params.partnership.duration[bond].bins
-            for bins in dur_bins:
-                if bins > 1:
-                    weights.append(dur_bins[bins].prob - dur_bins[bins - 1].prob)
-                else:
-                    weights.append(dur_bins[bins].prob)
-                vals.append(np.average([dur_bins[bins].min, dur_bins[bins].max]))
-            mean_rel_duration[bond] = np.average(vals, weights=weights)
-        else:
-            mean_rel_duration[bond] = params.partnership.duration[
-                bond
-            ].distribution.mean
-        assert mean_rel_duration[bond] > 0, "All bonds must have a positive duration!"
+        mean_rel_duration[bond] = {}
+        for race in params.classes.races:
+            if params.partnership.duration[bond][race].type == "bins":
+                weights = []
+                vals = []
+                dur_bins = params.partnership.duration[bond][race].bins
+                for bins in dur_bins:
+                    if bins > 1:
+                        weights.append(dur_bins[bins].prob - dur_bins[bins - 1].prob)
+                    else:
+                        weights.append(dur_bins[bins].prob)
+                    vals.append(np.average([dur_bins[bins].min, dur_bins[bins].max]))
+                mean_rel_duration[bond][race] = np.average(vals, weights=weights)
+            else:
+                mean_rel_duration[bond][race] = params.partnership.duration[bond][
+                    race
+                ].distribution.mean
+            assert (
+                mean_rel_duration[bond][race] > 0
+            ), "All bonds must have a positive duration!"
 
     return mean_rel_duration
 
 
 def get_partnership_duration(
-    params: "parse_params.ObjMap", rand_gen, bond_type: str
+    params: "parse_params.ObjMap", rand_gen, bond_type: str, race: Optional[str]
 ) -> int:
     """
     Get duration of a relationship drawn from bins or a distribution per the params [params.partnership.duration]
@@ -161,8 +165,8 @@ def get_partnership_duration(
         number of time steps the partnership should endure
     """
 
-    if params.partnership.duration[bond_type].type == "bins":
-        dur_info = params.partnership.duration[bond_type].bins
+    if params.partnership.duration[bond_type][race].type == "bins":
+        dur_info = params.partnership.duration[bond_type][race].bins
 
         diceroll = rand_gen.random()
         dur_bin = dur_info[5]
@@ -174,7 +178,7 @@ def get_partnership_duration(
         duration = rand_gen.randint(dur_bin.min, dur_bin.max)
 
     else:
-        dist = params.partnership.duration[bond_type].distribution
+        dist = params.partnership.duration[bond_type][race].distribution
         duration = utils.safe_dist(dist, rand_gen)
 
     return duration
diff --git a/titan/population.py b/titan/population.py
index b9175b6d..64ddaba0 100644
--- a/titan/population.py
+++ b/titan/population.py
@@ -91,7 +91,7 @@ def __init__(self, params: "parse_params.ObjMap", id: Optional[str] = None):
         self.relationships: Set["ag.Relationship"] = set()
 
         # find average partnership durations
-        self.mean_rel_duration: Dict[str, int] = partnering.get_mean_rel_duration(
+        self.mean_rel_duration: Dict[str, Dict] = partnering.get_mean_rel_duration(
             self.params
         )
 
@@ -191,7 +191,7 @@ def create_agent(
                 utils.safe_dist(dist_info, self.np_random)
                 * utils.safe_divide(
                     agent.location.params.calibration.sex.partner,
-                    self.mean_rel_duration[bond],
+                    self.mean_rel_duration[bond][race],
                 )
             )
             # so not zero if added mid-year
@@ -353,8 +353,9 @@ def update_agent_partners(
         no_match = True
 
         if partner:
+            race = utils.safe_random_choice([agent.race, partner.race], self.pop_random)
             duration = partnering.get_partnership_duration(
-                agent.location.params, self.np_random, bond_type
+                agent.location.params, self.np_random, bond_type, race
             )
             relationship = ag.Relationship(
                 agent, partner, duration, bond_type=bond_type
diff --git a/titan/population_io.py b/titan/population_io.py
index 4a66d71a..c8a095c2 100644
--- a/titan/population_io.py
+++ b/titan/population_io.py
@@ -54,7 +54,7 @@ def write(pop: Population, dir: str, compress: bool = True) -> str:
     returns:
         path, or archive name if compress is true
     """
-    assert len(pop.relationships) > 0, "can't write empty population"
+    assert len(pop.relationships) > 0, "Can't write empty population"
 
     # open agent file
     agent_file = os.path.join(dir, f"{pop.id}_agents.csv")
diff --git a/run_titan.py b/titan/run_titan.py
similarity index 94%
rename from run_titan.py
rename to titan/run_titan.py
index 8950c45d..e5575f6c 100755
--- a/run_titan.py
+++ b/titan/run_titan.py
@@ -5,6 +5,7 @@
 from copy import copy
 import sys
 import os
+from inspect import getsourcefile
 import shutil
 import argparse
 import itertools
@@ -15,15 +16,22 @@
 from typing import List, Optional
 import subprocess
 
+# allow imports to work if running it as a script for development locally
+if __name__ == "__main__":
+    PACKAGE_PARENT = ".."
+    SCRIPT_DIR = os.path.dirname(
+        os.path.realpath(os.path.join(os.getcwd(), os.path.expanduser(__file__)))
+    )
+    sys.path.append(os.path.normpath(os.path.join(SCRIPT_DIR, PACKAGE_PARENT)))
+
 from titan.model import TITAN
 from titan.population import Population
 import titan.population_io as pop_io
 from titan.parse_params import create_params
 from titan import utils
 
-# how many cores can we use
-NCORES = os.environ.get("SLURM_CPUS_PER_TASK", cpu_count())
-NCORES = int(NCORES)  # environment variable returns string
+# how many cores can we use, environment variable returns string
+NCORES = int(os.environ.get("SLURM_CPUS_PER_TASK", cpu_count()))
 
 # set up args parsing
 parser = argparse.ArgumentParser(description="Run TITAN model")
@@ -90,7 +98,7 @@ def sweep_range(string):
         except ValueError:
             raise ValueError("start, stop, and step must have same type (int or float)")
 
-    return {"param": parts[0], "start": start, "stop": stop, "step": step}
+    return {"param": parts[0].strip(), "start": start, "stop": stop, "step": step}
 
 
 parser.add_argument(
@@ -339,16 +347,10 @@ def main(
 
     # generate params - if no setting, set to none
     setting = setting.lower()
-    if setting == "custom":
-        setting = None
-    else:
-        setting = os.path.join(
-            os.path.dirname(os.path.abspath(__file__)), "settings", setting
-        )
-        assert os.path.isdir(setting), f"{setting} is not a directory"
+    setting_parsed = None if setting == "custom" else setting
 
     params = create_params(
-        setting,
+        setting_parsed,
         params_path,
         outfile_dir,
         error_on_unused=error_on_unused,
@@ -411,7 +413,7 @@ def mean(seq):
     print(f"all tasks - total: {toc} seconds")
 
 
-if __name__ == "__main__":
+def script_init():
     args = parser.parse_args()
     rows = args.rows.strip() if args.rows is not None else None
     sweepfile = args.sweepfile.strip() if args.sweepfile is not None else None
@@ -429,3 +431,7 @@ def mean(seq):
         save_pop=args.savepop,
         pop_path=poppath,
     )
+
+
+if __name__ == "__main__":
+    script_init()
diff --git a/settings/atlanta/assort_mix.yml b/titan/settings/atlanta/assort_mix.yml
similarity index 100%
rename from settings/atlanta/assort_mix.yml
rename to titan/settings/atlanta/assort_mix.yml
diff --git a/settings/atlanta/calibration.yml b/titan/settings/atlanta/calibration.yml
similarity index 100%
rename from settings/atlanta/calibration.yml
rename to titan/settings/atlanta/calibration.yml
diff --git a/settings/atlanta/demographics.yml b/titan/settings/atlanta/demographics.yml
similarity index 91%
rename from settings/atlanta/demographics.yml
rename to titan/settings/atlanta/demographics.yml
index 9bc31445..84238956 100644
--- a/settings/atlanta/demographics.yml
+++ b/titan/settings/atlanta/demographics.yml
@@ -11,11 +11,13 @@ demographics:
             versatile: 0.437
             insertive: 0.242
             receptive: 0.321
-        safe_sex: 0.688
+        safe_sex:
+          Sex: 
+            prob: 0.688
         prep:
           discontinue: 0.0
           adherence: 0.568
-          target: 0.258
+          cap: 0.258
           init: 0.258
         drug_type:
             NonInj:
@@ -36,7 +38,7 @@ demographics:
                   init: 0.232
               haart: &black_haart
                 init: 0.625
-                prob: 0.35
+                cap: 0.35
                 adherence:
                   init: 0.885
                   prob: 0.885
@@ -56,10 +58,12 @@ demographics:
             versatile: 0.544
             insertive: 0.228
             receptive: 0.228
-        safe_sex: 0.528
+        safe_sex:
+          Sex:
+            prob: 0.528
         prep:
           adherence: 0.911
-          target: 0.415
+          cap: 0.415
           discontinue: 0.0
           init: 0.415
         drug_type:
@@ -78,7 +82,7 @@ demographics:
               aids: 34.4
             haart: &white_haart
               init: 0.585
-              prob: 0.20
+              cap: 0.20
               adherence:
                 init: 0.817
                 prob: 0.817
diff --git a/settings/atlanta/model.yml b/titan/settings/atlanta/model.yml
similarity index 100%
rename from settings/atlanta/model.yml
rename to titan/settings/atlanta/model.yml
diff --git a/settings/atlanta/outputs.yml b/titan/settings/atlanta/outputs.yml
similarity index 100%
rename from settings/atlanta/outputs.yml
rename to titan/settings/atlanta/outputs.yml
diff --git a/settings/atlanta/partnership.yml b/titan/settings/atlanta/partnership.yml
similarity index 59%
rename from settings/atlanta/partnership.yml
rename to titan/settings/atlanta/partnership.yml
index 21d1d610..5a479b6d 100644
--- a/settings/atlanta/partnership.yml
+++ b/titan/settings/atlanta/partnership.yml
@@ -1,20 +1,22 @@
 partnership:
   duration:
     Sex:
-      type: bins
-      bins:
-        1:
-          prob: 0.456
-          min: 1
-          max: 3
-        2:
-          prob: 0.756
-          min: 3
-          max: 12
-        3:
-          prob: 1.0
-          min: 13
-          max: 24
+      white: &partnership_duration
+        type: bins
+        bins:
+          1:
+            prob: 0.456
+            min: 1
+            max: 3
+          2:
+            prob: 0.756
+            min: 3
+            max: 12
+          3:
+            prob: 1.0
+            min: 13
+            max: 24
+      black: *partnership_duration
   sex:
     frequency:
       Sex:
diff --git a/settings/chicago/chicago_baseCase.yml b/titan/settings/chicago/chicago_baseCase.yml
similarity index 79%
rename from settings/chicago/chicago_baseCase.yml
rename to titan/settings/chicago/chicago_baseCase.yml
index 7acd63b1..dc37cf19 100644
--- a/settings/chicago/chicago_baseCase.yml
+++ b/titan/settings/chicago/chicago_baseCase.yml
@@ -37,9 +37,6 @@ features:
 calibration:
   injection:
     act: 1.0
-  sex:
-    partner: 1.0
-    act: 1.0
   acquisition: 1.0
   test_frequency: 1.0
   mortality: 1.0
@@ -84,7 +81,7 @@ prep:
   type:
   - Oral
   - Inj
-  target: 0.088
+  cap: 0.088
   init: 0.088
   start_time: 0
   efficacy:
@@ -102,14 +99,10 @@ demographics:
         incar:
           init: 0.0
           prob: 0.0
-        safe_sex: 0.312
-        injection:
-          unsafe_prob: 0.27
-          num_acts: 5.0
         prep:
           discontinue: 0.0
           adherence: 0.568
-          target: 0.5
+          cap: 0.5
           init: 0.5
         high_risk:
           init: 0.0
@@ -144,34 +137,29 @@ demographics:
 partnership:
   duration:
     Social:
-      type: bins
-      bins:
-        1:
-          prob: 0.585
-          min: 1
-          max: 6
-        2:
-          prob: 0.701
-          min: 7
-          max: 12
-        3:
-          prob: 0.822
-          min: 13
-          max: 24
-        4:
-          prob: 0.8819999999999999
-          min: 25
-          max: 36
-        5:
-          prob: 1.0
-          min: 37
-          max: 48
-  sex:
-    acquisition:
-      MSM:
-        versatile: 0.00745
-        insertive: 0.0011
-        receptive: 0.0138
+      black:
+        type: bins
+        bins:
+          1:
+            prob: 0.585
+            min: 1
+            max: 6
+          2:
+            prob: 0.701
+            min: 7
+            max: 12
+          3:
+            prob: 0.822
+            min: 13
+            max: 24
+          4:
+            prob: 0.8819999999999999
+            min: 25
+            max: 36
+          5:
+            prob: 1.0
+            min: 37
+            max: 48
   pca:
     frequency:
       Social:
diff --git a/settings/mississippi/demographics.yml b/titan/settings/mississippi/demographics.yml
similarity index 70%
rename from settings/mississippi/demographics.yml
rename to titan/settings/mississippi/demographics.yml
index fd0989db..4d478e44 100644
--- a/settings/mississippi/demographics.yml
+++ b/titan/settings/mississippi/demographics.yml
@@ -9,7 +9,9 @@ demographics:
             versatile: 0.671
             insertive: 0.169
             receptive: 0.160
-        safe_sex: 0.214
+        safe_sex:
+          Sex:
+            prob: 0.214
         prep:
           discontinue: 0.034
           adherence: 0.860
@@ -25,7 +27,21 @@ demographics:
                 init: 0.46
             haart:
               init: 0.690
-              prob: 0.057
+              enroll:
+                enroll_0:
+                  prob: 0.609
+                  start: 0
+                  stop: 1
+                enroll_1:
+                  prob: 0.074
+                  start: 1
+                  stop: 12
+                enroll_2:
+                  prob: 0.0
+                  start: 12
+                  stop: 9999
+              reinit:
+                prob: 0.01
               adherence:
                 init: 0.500
                 prob: 0.500
diff --git a/settings/mississippi/model.yml b/titan/settings/mississippi/model.yml
similarity index 80%
rename from settings/mississippi/model.yml
rename to titan/settings/mississippi/model.yml
index e3bb5414..9a9f2201 100644
--- a/settings/mississippi/model.yml
+++ b/titan/settings/mississippi/model.yml
@@ -57,24 +57,25 @@ partnership:
         versatile: 0.0026625
   duration:
     Sex:
-      type: distribution
-      distribution:
-        dist_type: weibull_modified
-        vars:
-          1:
-            value: 0.586
-            value_type: float
-          2:
-            value: 11.532
-            value_type: float
-        mean: 16
+      black:
+        type: distribution
+        distribution:
+          dist_type: weibull_modified
+          vars:
+            1:
+              value: 0.586
+              value_type: float
+            2:
+              value: 11.532
+              value_type: float
+          mean: 16
 
 prep:
   type:
     - Oral
-  target: 0.049
+  cap: 0.049
   init: 0.25
-  target_as_prob: true
+  cap_as_prob: true
   efficacy:
     adherent: 0.96
     non_adherent: 0.83
diff --git a/settings/nyc-msm/demographics.yml b/titan/settings/nyc-msm/demographics.yml
similarity index 65%
rename from settings/nyc-msm/demographics.yml
rename to titan/settings/nyc-msm/demographics.yml
index 99096618..b866c00b 100644
--- a/settings/nyc-msm/demographics.yml
+++ b/titan/settings/nyc-msm/demographics.yml
@@ -9,11 +9,15 @@ demographics:
             versatile: 0.200
             insertive: 0.480
             receptive: 0.320
-        safe_sex: 0.275
+        safe_sex:
+          Main:
+            prob: 0.275
+          Casual:
+            prob: 0.409
         prep:
           discontinue: 0.034  # calibration
           adherence: 0.565
-          target: 0.028
+          cap: 0.028
           init: 0.252
         drug_type:
           None:
@@ -27,11 +31,30 @@ demographics:
                 init: 0.500
             haart:
               init: 0.764
-              prob: 0.212
+              enroll:
+                enroll_0:
+                  start: 0
+                  stop: 1
+                  prob: 0.709
+                enroll_1:
+                  start: 1
+                  stop: 3
+                  prob: 0.212
+                enroll_2:
+                  start: 3
+                  stop: 12
+                  prob: 0.051
+                enroll_3:
+                  start: 12
+                  stop: 9999
+                  prob: 0.0
+              reinit:
+                prob: 0.035
               adherence:
                 init: 0.489
                 prob: 0.489
-              discontinue: 0.0076
+                discontinue: 0.0689
+              discontinue: 0.014
             death_rate:
               base: 1.512
             num_partners:
@@ -63,11 +86,15 @@ demographics:
             insertive: 0.220
             receptive: 0.195
             versatile: 0.585
-        safe_sex: 0.262
+        safe_sex:
+          Main:
+            prob: 0.183
+          Casual:
+            prob: 0.341
         prep:
           discontinue: 0.025  # calibration
           adherence: 0.719
-          target: 0.026
+          cap: 0.026
           init: 0.234
         drug_type:
           None:
@@ -81,10 +108,29 @@ demographics:
                 init: 0.487
             haart:
               init: 0.764
-              prob: 0.193
+              enroll:
+                0:
+                  prob: 0.278
+                  start: 0
+                  stop: 1
+                1:
+                  prob: 0.193
+                  start: 1
+                  stop: 3
+                2:
+                  prob: 0.037
+                  start: 3
+                  stop: 12
+                3:
+                  start: 12
+                  stop: 9999
+                  prob: 0.0
+              reinit:
+                prob: 0.032
               adherence:
                 init: 0.719
                 prob: 0.719
+                discontinue: 0.0115
               discontinue: 0.0069  # calibration
             death_rate:
               base: 0.792
@@ -112,7 +158,11 @@ demographics:
     sex_type:
       MSM:
         ppl: 1.0
-        safe_sex: 0.126
+        safe_sex:
+          Main:
+            prob: 0.126
+          Casual:
+            prob: 0.277
         sex_role:
           init:
             insertive: 0.439
@@ -121,7 +171,7 @@ demographics:
         prep:
           discontinue: 0.014
           adherence: 0.738
-          target: 0.031
+          cap: 0.031
           init: 0.279
         drug_type:
           None:
@@ -135,11 +185,30 @@ demographics:
                 init: 0.471
             haart:
               init: 0.791
-              prob: 0.163
+              enroll:
+                0:
+                  start: 0
+                  stop: 1
+                  prob: 0.742
+                1:
+                  start: 1
+                  stop: 3
+                  prob: 0.163
+                2:
+                  start: 3
+                  stop: 12
+                  prob: 0.029
+                3:
+                  start: 12
+                  stop: 9999
+                  prob: 0.0
+              reinit:
+                prob: 0.041
               adherence:
                 init: 0.707
                 prob: 0.707
-              discontinue: 0.0059
+                discontinue: 0.0745
+              discontinue: 0.00883
             death_rate:
               base: 0.0696
             num_partners:
diff --git a/settings/nyc-msm/hiv.yml b/titan/settings/nyc-msm/hiv.yml
similarity index 81%
rename from settings/nyc-msm/hiv.yml
rename to titan/settings/nyc-msm/hiv.yml
index 53c0f32a..73445206 100644
--- a/settings/nyc-msm/hiv.yml
+++ b/titan/settings/nyc-msm/hiv.yml
@@ -9,8 +9,11 @@ hiv:
 prep:
   target_model:
     - Racial
-  target_as_prob: true
+  cap_as_prob: true
   start_time: -48
   efficacy:
     adherent: 0.96
     non_adherent: 0.76
+
+haart:
+  use_reinit: true
diff --git a/titan/settings/nyc-msm/location.yml b/titan/settings/nyc-msm/location.yml
new file mode 100644
index 00000000..8fc067b0
--- /dev/null
+++ b/titan/settings/nyc-msm/location.yml
@@ -0,0 +1,55 @@
+location:
+  scaling:
+    high_test:
+      demographics|white|ppl:
+        field: override
+        override: 0.384
+      demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: &high_test_prob
+        field: override
+        override: 0.333
+      demographics|black|ppl:
+        field: override
+        override: 0.278
+      demographics|black|sex_type|MSM|drug_type|None|hiv|dx|prob: *high_test_prob
+      demographics|latino|ppl:
+        field: override
+        override: 0.338
+      demographics|latino|sex_type|MSM|drug_type|None|hiv|dx|prob: *high_test_prob
+
+    mid_test:
+      demographics|white|ppl:
+        field: override
+        override: 0.587
+      demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: &mid_test_prob
+        field: override
+        override: 0.167
+      demographics|black|ppl:
+        field: override
+        override: 0.187
+      demographics|black|sex_type|MSM|drug_type|None|hiv|dx|prob: *mid_test_prob
+      demographics|latino|ppl:
+        field: override
+        override: 0.226
+      demographics|latino|sex_type|MSM|drug_type|None|hiv|dx|prob: *mid_test_prob
+
+    low_test:
+      demographics|white|ppl:
+        field: override
+        override: 0.605
+      demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: &low_test_prob
+        field: override
+        override: 0.042
+      demographics|black|ppl:
+        field: override
+        override: 0.082
+      demographics|black|sex_type|MSM|drug_type|None|hiv|dx|prob: *low_test_prob
+      demographics|latino|ppl:
+        field: override
+        override: 0.313
+      demographics|latino|sex_type|MSM|drug_type|None|hiv|dx|prob: *low_test_prob
+
+  edges:
+    edge_default:
+      location_1: high_test
+      location_2: high_test
+      distance: 0
\ No newline at end of file
diff --git a/settings/nyc-msm/model.yml b/titan/settings/nyc-msm/model.yml
similarity index 90%
rename from settings/nyc-msm/model.yml
rename to titan/settings/nyc-msm/model.yml
index e2c0dd92..517c68f0 100644
--- a/settings/nyc-msm/model.yml
+++ b/titan/settings/nyc-msm/model.yml
@@ -27,6 +27,14 @@ classes:
         - sex
   drug_types:
     - None
+  locations:
+    high_test:
+      ppl: .190
+    mid_test:
+      ppl: .634
+    low_test:
+      ppl: .176
+
   
 features:
   prep: true
diff --git a/titan/settings/nyc-msm/partnership.yml b/titan/settings/nyc-msm/partnership.yml
new file mode 100644
index 00000000..fb566253
--- /dev/null
+++ b/titan/settings/nyc-msm/partnership.yml
@@ -0,0 +1,111 @@
+partnership:
+  sex:
+    frequency:
+      Main:
+        type: distribution
+        distribution:
+          dist_type: gamma
+          vars:
+            1:
+              value: 0.439
+              value_type: float
+            2:
+              value: 15.3
+              value_type: float
+      Casual:
+        type: distribution
+        distribution:
+          dist_type: gamma
+          vars:
+            1:
+              value: 0.131
+              value_type: float
+            2:
+              value: 16.5
+              value_type: float
+    haart_scaling:
+      MSM: # calibration
+        non_adherent: 0.165
+        adherent: 0.00
+    acquisition:
+      MSM:
+        insertive: 0.0017
+        receptive: 0.0075
+        versatile: 0.0046
+
+  duration:
+    Main:
+      white:
+        type: distribution
+        distribution:
+          dist_type: wald
+          vars:
+            1:
+              value: 70.44
+              value_type: float
+            2:
+              value: 6.72
+              value_type: float
+          mean: 70.44
+      black:
+        type: distribution
+        distribution:
+          dist_type: wald
+          vars:
+            1:
+              value: 20.88
+              value_type: float
+            2:
+              value: 2.76
+              value_type: float
+          mean: 20.88
+      latino:
+        type: distribution
+        distribution:
+          dist_type: wald
+          vars:
+            1:
+              value: 35.52
+              value_type: float
+            2:
+              value: 3.84
+              value_type: float
+          mean: 3.84
+    Casual:
+      white:
+        type: distribution
+        distribution:
+          dist_type: wald
+          vars:
+            1:
+              value: 11.76
+              value_type: float
+            2:
+              value: 1.32
+              value_type: float
+          mean: 11.76
+      black:
+        type: distribution
+        distribution:
+          dist_type: wald
+          vars:
+            1:
+              value: 17.16
+              value_type: float
+            2:
+              value: 1.56
+              value_type: float
+          mean: 17.16
+      latino:
+        type: distribution
+        distribution:
+          dist_type: wald
+          vars:
+            1:
+              value: 16.32
+              value_type: float
+            2:
+              value: 1.20
+              value_type: float
+          mean: 16.32
+
diff --git a/settings/scott/demographics.yml b/titan/settings/scott/demographics.yml
similarity index 83%
rename from settings/scott/demographics.yml
rename to titan/settings/scott/demographics.yml
index ce8b837c..045142a7 100644
--- a/settings/scott/demographics.yml
+++ b/titan/settings/scott/demographics.yml
@@ -24,7 +24,11 @@ demographics:
         sex_role:
           init:
             insertive: 1.0
-        safe_sex: 0.1
+        safe_sex:
+          Sex: &condom_use_HM
+            prob: 0.1
+          Inj: *condom_use_HM
+          SexInj: *condom_use_HM
         injection:
           unsafe_prob: 0.321
           num_acts: 5
@@ -36,9 +40,13 @@ demographics:
               dx:
                 prob: 0.202
                 init: 1.0
-            haart:
+            haart: &haart_vals
               init: 1.0
-              prob: 0.679
+              enroll:
+                enroll_0:
+                  prob: 0.679
+                  start: 0
+                  stop: 999
               adherence:
                 init: 1.0
                 prob: 1.0
@@ -82,13 +90,7 @@ demographics:
               hiv: 3.1
               aids: 10.4
               haart_adherent: 1.0
-            haart:
-              init: 1.0
-              prob: 0.679
-              adherence:
-                init: 1.0
-                prob: 1.0
-              discontinue: 0.000
+            haart: *haart_vals
             num_partners:
               Sex:
                 dist_type: poisson
@@ -101,7 +103,11 @@ demographics:
         sex_role:
           init:
             receptive: 1.0
-        safe_sex: 0.2
+        safe_sex:
+          Sex: &condom_use_HF
+            prob: 0.2
+          Inj: *condom_use_HF
+          SexInj: *condom_use_HF
         injection:
           unsafe_prob: 0.321
           num_acts: 5
diff --git a/settings/scott/model.yml b/titan/settings/scott/model.yml
similarity index 86%
rename from settings/scott/model.yml
rename to titan/settings/scott/model.yml
index c21faf8d..45ca3646 100644
--- a/settings/scott/model.yml
+++ b/titan/settings/scott/model.yml
@@ -43,12 +43,14 @@ hiv:
   dx:
     risk_reduction:
       sex: 0.19
-  haart_cap: true
   start_time: -48
   init: -48
   aids:
     prob: 0.0029
 
+haart:
+  use_cap: true
+
 timeline_scaling:
   timeline:
     burn_scale:
@@ -180,35 +182,38 @@ partnership:
         adherent: 0.06
   duration:
     Sex:
-      type: distribution
-      distribution:
-        dist_type: set_value
-        vars:
-          1:
-            value: 12100
-            value_type: int
-        mean: 12100
+      white:
+        type: distribution
+        distribution:
+          dist_type: set_value
+          vars:
+            1:
+              value: 12100
+              value_type: int
+          mean: 12100
     SexInj:
-      type: distribution
-      distribution:
-        dist_type: set_value
-        vars:
-          1:
-            value: 121
-            value_type: int
-        mean: 121
+      white:
+        type: distribution
+        distribution:
+          dist_type: set_value
+          vars:
+            1:
+              value: 121
+              value_type: int
+          mean: 121
     Inj:
-      type: distribution
-      distribution:
-        dist_type: gamma
-        vars:
-          1:
-            value: 5.37
-            value_type: float
-          2:
-            value: 23.28
-            value_type: float
-        mean: 125
+      white:
+        type: distribution
+        distribution:
+          dist_type: gamma
+          vars:
+            1:
+              value: 5.37
+              value_type: float
+            2:
+              value: 23.28
+              value_type: float
+          mean: 125
 
 assort_mix:
   assort_pwid:
diff --git a/titan/utils.py b/titan/utils.py
index 6de0d151..b218df56 100644
--- a/titan/utils.py
+++ b/titan/utils.py
@@ -176,7 +176,7 @@ def get_param_from_path(params, param_path, delimiter):
 
 def scale_param(params, param_path, scalar, delimiter="|"):
     """
-    Given the params and a parameter path in the format prep|target, scale the
+    Given the params and a parameter path in the format prep|cap, scale the
     current value by the scalar
     """
     scaling_item, last_key = get_param_from_path(params, param_path, delimiter)
@@ -188,7 +188,7 @@ def scale_param(params, param_path, scalar, delimiter="|"):
 
 def override_param(params, param_path, value, delimiter="|"):
     """
-    Given the params and a parameter path in the format prep|target, change the
+    Given the params and a parameter path in the format prep|cap, change the
     current value to new value
     """
     override_item, last_key = get_param_from_path(params, param_path, delimiter)